XJ650 Starting issues

Hello!

I have inherited an 1982 XJ650J from my father, after having got my motorcycle license recently (last month, having taken the MSF course).
It had some work done on it 10 years ago, was registered back then, and presumably was running. New tires, oil, airfilter, etc. Dad said it had some idling problems but to just give it some choke to start with and let it warm up, pretty standard stuff for a carborated motorcycle, I think.

When I got the bike, dad had trickle charged it and I went to try it out, and it wouldn’t turn over, but the starter would make noise, and demonstrating this to my girlfriend, she mentioned it had compression and that was a good sign.

I ended up bringing it to a motorcycle repair guy who was willing to work on it, since most wouldn’t touch anything this old (I have some mechanical knowledge, with cars, namely repairing/fixing the front suspension and that sort of thing, but I don’t have access to a garage, nor was I confident enough to futz around with a 43 year old bike and break something more) and he addressed a few things:
“no spark on 1 & 4 and repaired bad connection at ignition coil (has new spark plugs)”
“drained and flushed fuel system”
“installed new carb set rebuild kit adjusted & synchronized”
“new fuel (and conditioner)”
“repaired stripped oil filter housing and replaced housing orings”
“rebuilt front brake caliper, flushed and bled brake fluid”

This worked pretty well, I picked up the bike and drove it about 30 minutes back to my house, parking it in my friend’s garage, to where I’d later transport it to my girlfriend’s house (a further 35+ minutes drive away) to her garage so I could have a comfortable location to work on it more over the winter (cleaning, updating the electronics, moving it away from the vacuum tube fuses into something slightly more modern, keeping the style but adding some quality of life features to the bike, as I want to keep it and ride it all the time). Embarrassingly, as a new rider, I got a bit nervous at the intersections, dumping the clutch and struggling to start it back up properly, but eventually was able to continue driving it the rest of the way home. I noticed back then it was a little difficult to start at the intersection, but I just assumed that was user error, not motorcycle’s fault.

I turned the bike off at her house, kickstand killswitch seems to work to shut off the motorcycle, though I noticed I had left the right hand control module on the “on” position, the bike was off (not sure if this matters), and parked the bike Sunday.

Come today, I pull it out of the garage to start it, and move it elsewhere, and she starts up without much issue, and I take off down the neighborhood, riding it in first gear, wanting to just lazily take my time driving back to my house. I get to an intersection about a quarter mile away (if that), slow down, pull in the clutch, apply both brakes, check to see if I can enter the intersection, and start to take off, being intentionally careful with the clutch, and the bike seemed fine… for a few seconds, and then as I straightened out it just stalls. Okay, I think, maybe I just dumped the clutch or something even though I’m being careful, and go to start the bike again.

This time however, the bike struggles to start up, I notice when I try to start, the oil light comes on, and the starter does not make noise. I fiddle around with it a bit and get it to start for a second, and it dies again, not having let off the clutch at all this time. The choke is still on a bit, I think. I was going to turn it off once I had got on the road, so I fiddle around some more, and the bike still doesn’t start, and the starter does not make noise. The Instrument cluster is backlit, and the lights for Neutral/Blinkers/Oil come up (oil light comes on when starter pressed, goes away when released)

Doing some research, I think, maybe the kickstand killswitch wire is causing the bike to not start up, so I engage/disengage it, no change. I check other things, like the petcock, which is switched to ON, try switching it to reserve, no change. Check the gas, looks like it’s about 75% full? I’m not 100% sure, but I assume there should be plenty. Repair guy says the oils all look good, from when he looked at it, and I couldn’t see any leaks anywhere.

At this point I give up, roll the bike back to my friend’s garage. I went and I got a trickle charger, and there’s a place nearby that has a replacement battery I can try to buy, because it sounds like maybe it could just be the battery is old, it’s possible it’s 10-15 years old, but if that doesn’t work then I’m not really sure what the issue is.

I would appreciate any suggestions y’all have, I really am in love with this bike and it was running great, and I’m a bit disappointed it suddenly stopped working.

 

Welcome to the forum. You should check when you can get the bike is running by putting a multimeter measuring 20V DC on the terminals of the battery, and and get an assistant to press the starter button. The voltage must not drop below 10.5 volts or the plugs won't spark. You are looking for around 14.5 volts if the alternator is charging. Do you have the glass fuses they are problematic the clips break and you are better off with a blade type fuse holder.
So you have a spark on all four now after the mechanic did the repair. ?
Do you mean the carburettors were cleaned, or replaced and new parts fitted?
Is your fuel tank really clean.
Sidestand switch the engine should not run with the stand down.
There are small cold start jets in the bottom of the float bowls, did your mechanic make sure these were all clear?

 

So, a bunch of things happened:

Bought a new battery, since I figured there was a problem with the old battery, since it was 10-15 years old (expiration on it said 2018) and charged it up, also charging up the old battery.

Tested the old battery, and it came on when fully charged. Swapped out the old battery anyways for a brand new one (Lead, not AGM, 12N12A-4A-1) and the bike started right up without any issues. I do plan eventually to buy a MB12U 12V AGM for the bike.

I then proceeded to drive it home, about 5 miles away, everything was great. Except in my hubris I was going a little too fast right before I needed to slow down and make a left turn, trying to brake and downshifting (perhaps downshifting too much), I was able to bring it to a complete stop, but not before I kind of got it stopped on the front wheel near my apartment on a curb, front wheel slightly raised in the dirt, and I lost my center of balance and the bike fell over on it’s left. I was fine, and either the bike shut off, or I hit the killswitch without thinking. The bike has the attachment on it for a crash bar, that sticks out farther than the engine, but no crash bar itself, so kinda like a mini frame slider?

Tried turning the bike on, and it would not turn on at all this time. No lights on the instrument cluster at all this time. I parked the bike for the day, fearing I had damaged it by it tipping over.

Today, I bought my girlfriend over, we took a multimeter to it and checked all the fuses (okay) and noticed the battery, the new one, was hovering around 11V (we had the key in the ignition but it wasn’t set to “on” it was simply in the ignition, so we took the battery out and stuck it on my trickle charger I just bought the day before. After the battery was charged, we tried turning the bike on, but no change in behavior, instrument cluster still wouldn’t turn on, and starter didn’t do anything. We traced the connection points between the battery and each of the instrument cluster, relays, key, etc, and were very confused because everything had a nice solid trace with the multimeter (we also have the original Yamaha manual that has the circuit diagrams). Then, as she was rubbing one of the probes on the edge of the vacuum fuses from the various points in the front of the bike, I heard a noise like there was some sort of electrical connection happening somewhere. We noticed this, and decided to connect everything but the headlight and it fired right up!

I hopped on and drove to the end of the parking lot, started to slow down to do a u-turn, and it shut off again. At this point we were like, okay, something is messed up, and we took the battery out, cleaned the positive and negative cables on the battery end, and unscrewed the negative cable from the engine block and cleaned that too with a water/baking soda mix and a wire brush until the connection tips were shiny. We still had a good charge on the battery with the multimeter.

I was able to start her up again and she seemed fine, working as expected. The bike definitely needs some time to warm up after not running for a little bit, once she’s warmed up, she seems to run around 500-600 rpms with the choke off, which seems a bit low to me. The GF says this is probably running a bit lean?

One new thing I noticed that was new, is that sometimes when in neutral and shifting into first, I get a bit of resistance, and some clicking from the shifter. I rock back and forth a bit and try shifting it into first, I get a clunk, and then it’s fine. I’m not sure if I should be worried about that or not.

I also wonder if the issues I’m having off and on with it “stalling” at weird times and even the new battery “losing power” mean there’s a drain somewhere, or maybe it’s something wrong with the “charging system”?

 

Welcome to the forum. Vintage bikes can be a challenge to get running properly especially after sitting for an extended time. That said it can be very rewarding to do the troubleshooting and repairs you will run across. Do yourself a favor and make changes one at a time and test the result. It's tempting to dive right in a change a bunch of things, but this usually just leads you further down the rabbit hole. Plus if you do get it running correctly you won't know which change fixed the problem. Be patient and take your time. Take lots of photos so you can find your way back when you disassemble things.

Best of luck with your "new" bike!

 

It sounds like you have found one of the problems with the electrical system...... the fuse panel. The clips that hold the fuses in get old and brittle and lose their spring and grip (like all of us) on the fuses. When you try to flex them back or take the fuses out to clean the contacts they break off. The cure is a new fuse panel for the blade type fuses. Not hard to do nor terribly expensive. Just a bit fussy. Len at XJ4EVER.com, just click on the logo on the upper right corner of these pages, has a nice kit to do this. A replacement fuse panel can be found at almost any auto parts store for under about $15. @BallAquatics is right, change 1 thing at a time so you know what works and what does not. Good luck and welcome, these are awesome bikes when right, I like them better than most of the new bikes.

 

I recently ordered from Len to replace the side fairing grommets (which are either missing or rotten) so once I get those in, I’ll likely just get the blade fuse kit and upgrade that next.

Next on the list is likely to swap the lights to LED to save some battery juice, and then the speedometer to a digital one. I’ll likely want to replace the right hand control module to a modern engine killswitch instead of this OFF|ON|OFF design, which I think is kind of peculiar and just adds a bit of confusion if you need to stop the engine for some reason in a hurry.

I might want to add some other grips if possible, heated grips would be cool if I can figure it out, along with some sort of way to attach my phone and charge it, but these are all like, ideas much farther down the road, to be fair.

 

Learning tons of new things about this bike every day, apparently the XJ650 idle screw needs to be adjusted to around 1050rpms, and there is a screw on the carbs, I wonder if I can reach it with the carbs already installed? I'll check later, since it seems to idle around 600rpm and that seemed a bit low to me, and if the spec is 1050rpm then that makes a hell of a lot of sense as to why it sounded sputtery.

 

The idle speed adjustment screw is between carbs 2 & 3 with a knob on it. Yes, you can reach it with the carbs on, easier if you have small hands and loose wrist joints. If the engine is well warmed up it will be hot in there and it will not be comfortable. Each carb also has an air mixture screw on the engine side (not the air box side) from the factory the screws are under a pressed in cap that likely needs to be adjusted for best idle, and then the carbs need to sycn'ed to each other again. It is all in the details! Lots of carb info here, scattered about. Good luck, have fun!

 

So if I change the idle speed adjustment screw, I have to also change the air mixture screws on the carbs and resync?

If so, that might have to wait till another time, I don't have the means to resync the carbs myself yet.

edit:
I'm thinking about if there's a way to add a fuel gauge to this bike, and it seems like there's a few options:
1. swap out 650 tank with a 750 tank that has a sending unit, including replacing speed/tach with something that supports it
2. homebrew a sending unit
3. buy a sending unit online somewhere?

3 would be best, but based on some googling it sounds like most just give up or swap out the tank with one that already has one, probably due to it being easier. Does this sound correct?

 

@RideAlong420 , not quite.... the idle speed adjustment between the carbs just adjusts the throttles by pushing them all open a tiny amount, it is a very fine thread. What I meant is that the air mixture screws and sync both have a dramatic effect on the quality of the idle. The more properly they are adjusted the better you can adjust the idle speed knob and have a nice, smooth, consistent idle and cleaner engine speed pick up off idle.
As far as a fuel gauge I guess you could add one to your bike but it would be a lot of wiring issues. The 750 tank on the 650 is nice because it adds a gallon of capacity and range. Maybe someone here has added the gauge function as well but I don't recall reading about it.

 

I've been riding it around in the parking lot, not at a high rpm because parking lot, and eventually the bike dies on me like before, like the battery ran out.

Should I check the brushes first, and clean every contact cable I can find? I already did the main battery positive and negative terminals.

 

Will it restart right away or do you have to recharge the battery? If you have a DMM check the voltage across the battery with the bike running. It should be 14.5V +/-.3V when RPM are raised to 2K and above with a fully charged battery.

 

When this happens I have to recharge the battery.

I can check with the DMM probably Tuesday

 

Did you get the blade fuse kit installed as suggested, and did you adjust the idle up to about 1000 RPM? Either one of those could cause the bike to stall out

 

Not yet, might be a few weeks before then

 

One easy adjustment to set your idle RPM, takes about a minute.

 

Congrats on saving the family bike. Just scanning through this thread, maybe some of this has been answered already:

It is normal for the oil light to come on with the start button. Seeing it light up then is a test to confirm it still works. The light is triggered by a float switch measuring oil level, not oil pressure. The oil switch does not affect the ignition circuit.

The clutch clunk is from the clutch discs dragging and still trying to spin the transmission even with the clutch lever pulled in. This isn't unexpected in a bike that sat for years, as often some corrosion will form on the top of the discs that aren't submerged in oil. This should smooth out in time. If not, you might plan a clutch change. It isn't an awful job if you read up on it and prepare. But first check the free play in the clutch cable to make sure you are getting all the throw available from the clutch lever. It isn't abnormal to have some clunk on cold oil, regardless of clutch condition.

If you intend to keep the bike long term, getting intimately familiar with the carbs is a good idea. There's lots of info on this site about cleaning, adjusting, synchronizing, how they work, etc. The "new carb set rebuild kit" from the mechanic could mean a lot of things. Factory jets should be cleaned, not replaced with Amazon kits. And you have an aftermarket exhaust, which throws another wrinkle into getting these tuned.

The bike dying while just riding around in first gear could be a lot of things, but fuses, relays, connections are the place to start and sounds like you are working on that.

If you don't have one already, get the Haynes manual.

 

One more follow up after thinking about this...if you are new to riding and still working on those smooth starts, don't be afraid to slip the clutch. The multi disc wet clutches in these (or almost any bike) are made to handle more slip and heat than a dry clutch in a Honda civic. Don't try to have the clutch fully released within a few bike lengths from the stop light. These motors are not happy trying to lug them down. Practice holding some mid-rpm throttle and letting the clutch do the work. The parking lot practice you are describing is great stuff. Just do a hundred starts and stops and the left hand eventually becomes a more instinctive part of power control. Dirt bikes are a great place to learn this also.

 

I have the original XJ650 Yamaha manual, is the Haynes manual worth it?

I haven’t been riding the clutch much, as you say, during my MSF I rode a Honda Rebel and I was told that I would eventually burn out the clutch if I kept the friction zone “half engaged”, so I’ve only dipped into it when I needed to deliver power, you’re saying it’s actually fine for this bike?

I’m certainly finding it easier and easier to be connected with the bike’s friction zone as I play more with it, at this point I don’t believe any of the stalls recently have been because I dumped the clutch. The very last time, the other day, I was riding back and forth in my parking lot, doing u turns, and I saw a car coming, I pulled in the clutch fully, came to a stop so that way I can just let the car go by, and as I was sitting there the bike sputtered and shut off, and couldn’t turn it back on again.

I haven’t had the chance to do anything with the bike this week, and probably won’t until Sunday afternoon at this point, frankly. My GF bought me some new vacuum fuses (just in case, they were cheap), so I’ll swap those over then, put the charged battery back in, and test the resistances as mentioned. I also got some stuff to try and find any contact points I possibly can, clean them with a steel brush and some corrosion cleaner, and condition them to make sure that’s not the case, at least on the battery terminal/ground cable, positive end. We already cleaned this (the ends had a nice brassy shine) but maybe there’s some more contact points I missed somewhere (we also scrubbed the fusebox ends where it holds the fuses, just in case)

I’m assuming the brushes have never been replaced (12,000 miles) but I’d need to open the alternator casing to measure them. I am not sure if this would need a new gasket or not to close it back up, but I’ll end up buying some brushes from the XJ store (along with the blade upgrade kit) probably in the next few weeks.

It also didn’t give me any issue with shifting into first, so maybe it was just a one-off

 

Don't worry about points in your ignition. These bikes have electronic ignition that is pretty bullet proof. The box does fail but it is so rare as to be a non-issue. Your bike does run so that pretty much eliminates that area of question. At 12k miles it is very unlikely you have alternator brush issues as well. Cleaning connections is a good step, use GREAT care is trying to clean the fuse panel clips and putting in the new blade fuse panel is a very good thing. Only change one thing at time otherwise you can get really confused as to what changed what symptom. I think your stalling issue is likely related to your low speed, low engine speed, low charging situation, depending on how long you were riding and practicing. In perfect condition these bikes do not produce enough electricity to charge the battery until 2500-3000 rpm and then that is still not much. When the battery charge level gets down it will still turn the engine over but not have enough energy left over to create a spark in a healthy ignition. I think charge your battery, replace the fuse panel, carefully clean the connections at the rectifier/ regulator and ride some more, as soon as you are comfortable. Just don't try to fix too much too quickly. And have fun!

 

How do you clean the “rectifier/regulator”? I cleaned the battery terminals (including the cable that connects to the engine block) and tried scrubbing the fuses, but they’re kinda curved and it’s hard to really get in there.

I charged up the battery, replaced the vacuum fuses with brand new ones my gf bought, started the bike with full choke, and let it idle a bit, mostly it was hovering around 3k rpm. I walked back to my car and at one point the idle increased on its own, and then climbed back down again. I thought the bike was warmed up enough, so I took the bike down the street to my gym, and ran it a bit with the choke on, slightly, to make sure the RPMs were a bit higher, to make sure there was enough charge going to the battery. I made it to the intersection, I slowed down, the engine was sputtering and eventually stalled. It took a try or two, and it started up, and I rode the rest of the way to the gym.

After leaving the gym, the bike was on half choke, it sputtered and “started” for a second when I turned it back on and it stalled again. The subsequent attempts failed to start the bike at all, the starter wasn’t clicking (or I can’t hear it), the only light that showed up was the neutral light, and the oil light when attempting to start.

So, I pushed the bike back to my apartment. I’ll take another look Sunday I guess.

 

@RideAlong420, not clean the Regulator/rectifier but it's contacts where the wiring harness plugs in. And make sure the connectors are not melted or otherwise damaged. If you have a digital multimeter check for AC output from the alternator. There are 3 white wires coming to the R/R that are the AC feed. I don't remember what the voltage on them should be but it should be 40 to 70 volts AC between all of the 3 wires in any configuration. AC in to the R/R and little to no DC out to the battery proves the R/R is bad. DC out to the battery proves it is not. Have you measured the DC at the battery when the bike is running? At 2500-3000 rpm it should be in the neighborhood of 14.5 VDC, otherwise you don't have enough electrical power to continue to run.

 

Sounds like multiple issues, which makes troubleshooting difficult. The engine just dying instantly while riding, if that is still happening, is more likely ignition, and chasing those electrical connections likely needed. Sputtering then dying sounds more like fuel. Your carbs might not be properly cleaned or synched. Out of synch will cause all kinds of problems trying to dial in the idle. I hate to suggest it when you are still obviously learning your way around the bike, but I'd be pulling the carbs and starting over. Or maybe take back to the mechanic and ask to check vacuum synch. If they will let you watch the process, even better. It's just really tough to say if the carbs got cleaned and synched properly unless you understand it and do it yourself. But it is a bit onerous when first starting on bike repair. Still keep troubleshooting your electrical first to rule that out before pulling carbs. Sometimes intermittent electrical issues can sound a lot like fuel issues.

THE MOST COMMON INTERMITTENT ELECTRICAL CONNECTION IS THE FUSES THEMSELVES! It's happened to me and I've seen it posted here more than once. Even with the fuses replaced, those stock fuse clips are corroded and weak. They might work fine, then hit a bump and oops...ignition power lost. So that blade fuse upgrade as previously mentioned is worth doing.

The last problem of the starter not engaging definitely has nothing to do with the carbs, but there are some things that can affect both the start circuit and ignition. If you get the oil light with the push button, you can rule out main key switch, kill switch (both provide power to the oil light in series) and start button (provides ground for the oil light). It also means you have power through the ignition circuit fuse. Next would be the start circuit cutoff relay. When you turn the key switch on, kill switch on, and bike in neutral, you should hear a faint click under the rear of the gas tank. With small fingers you can reach in under the tank, over the carbs, and feel the relay clicking. There is a second relay (sidestand) that will also be clicking with this test. It's under the tank, but further forward by the coils. To isolate only the start circuit relay, you can put it in gear (neutral light is off) with key switch and kill switch both on, and pull the clutch lever. If your clutch lever switch is working properly, only the start circuit relay will be clicking on/off.

You can also remove your seat, remove the rear tank mount bolt, and if there's enough slack in your fuel line, lift the rear of the tank to see the start circuit relay. Here's a photo of it from that view.



Here's a photo of the sidestand relay up near the coils.




If you feel the click on the start circuit cutoff relay (rear of the tank), that's good. If no click, either a bad relay or corroded connections. This relay is powered when either in neutral, or if not in neutral, when the sidestand is up AND the clutch lever is pulled in. Since your neutral light comes on, we'll assume your neutral switch (in the transmission) is working. When clicked ON, this relay provides power to the starter solenoid. Starter solenoid is under the right hand side cover...round thing with a couple big wires under rubber covers. To be clear, we're talking about two different relays...the start circuit cutoff relay under the rear of the tank, and the starter solenoid under the right hand side cover. Similar names, different relays.

Here's a photo with the right side cover removed. Starter solenoid is under the rubber covers to the left of the battery...rubber covers might have disappeared over the years.



Here's a photo with the covers removed.

You can confirm you have power to the starter solenoid via the start circuit cutoff relay with your multimeter if you check the red/white wire in the connector circled yellow below (key switch on, kill switch on, bike in neutral). You don't have to be pushing the start button to check for 12 volts on the red/white wire. Your starter button is providing a path to ground through the blue/white wire. The start button itself is likely still good since your oil light is coming on when pushed. Below you see the big wire (sort of a flat metal bus) on the starter solenoid hooked directly to the positive battery terminal. The other big wire is headed below to the starter. If you have 12 volts on the small red/white wire in the connector terminal, and no click of the solenoid itself when pushing the start button, you likely have a bad solenoid. If you do hear a click hear (you said no click, but just in case) the solenoid still might be bad, or the starter is bad. The quick and dirty test for the starter is to jump those two big wires (red arrows in photo below) on the solenoid with a screwdriver or wrench. It will spark, but the starter should turn over. If not, bad starter.

Of these things mentioned...start circuit cutoff relay, starter solenoid, and starter...the starter solenoid is most suspect.




If the solenoid is suspected, hold your start button down and smack the solenoid with a screwdriver or something. If this causes it to engage, replace it.

That aforementioned sidestand relay will ground out the TCI with the sidestand down when working properly, and the sidestand switch itself can shutoff the start circuit relay described above (but not in neutral). Areas for potential intermittent ignition issues. But that's probably enough to tackle for now. Sidestand relay and sidestand switch are not involved in the start relay as long as you are in neutral.

And your question about the manual...if its the owners manual that you currently have (small half sheet size booklet), yes the Haynes manual is worth it. It has good wiring diagrams and explanations of these relay circuits and how to test them.

Also descriptions of the relay circuits and testing here:

https://xjbikes.com/forums/threads/the-ultimate-relay-switch-sensor-and-diodes-guide.27543/

 

Haven't had time to test anything, but I'm gonna head over to the hardware store and buy some "electrical contact cleaner" spray and some di-electric grease (and ordered some ACF-50 spray too) so I can find every single molex connector on this damn bike and see if that helps.

I've also ordered the blade fusebox kit from Len and some extra accessory wires for when I later want to swap out the headlamp with a LED one to reduce power draw, and hook up stuff like heated grips or a phone charger, so I can do that whenever that comes in

 

This is the manual I have, it has circuit diagrams and step by step instructions. Doesn't seem to be missing anything.

 

oh heck yah! That's gold right there. The owners manual is the smaller booklet with just basic maintenance stuff.

 

I took off the bike chain that came with the motorcycle...I don't think it's ever been used in it's entire history. Was a bit of a pain to take out of the slot. Got myself some extra keys tho, I only had 1! Had to drive half an hour to find a locksmith willing to make me two copies.

Looks like my shipment from Len should show up tomorrow, so I'll plan for Saturday morning to get up early and plan on sitting outside in the parking lot at 44F weather while I uncover the bike and look over the entire wiring harness to see if there's any corrosion, using electrical contact cleaner, dielectric grease after, using some battery end cleaner/conditioner I got, and then get my wire stripper out and replace the fusebox with the new glow when blown blade fuses kit. Hopefully I won't be dumb and the bike will start after all that.

 

I'm starting to finally work on the bike now, I tested the voltage across the battery before I turned it on, at 12.66/7 that should be plenty enough to start the motorcycle.

I stick the key in, full choke, turn it on, starts up immediately, having sat for a week. I tested the voltage across the battery while I let it get up to around 3,000+ and took another photo.

I saw it get up to around 14.80v I think when I was just kind of just giving it a little bit of gas on the throttle

 

So far I've cleaned almost all of the wiring harness connectors,with electrical contact cleaner, and let it fully dry. And also some of the connections already have some dielectric grease on them, or at least some sort of grease on the cable connectors, namely around the rectifier regulator connectors

I've also cleaned the battery terminal ends with a battery cleaner terminal spray

 

I don't know if it's obvious from these photos, but there's a whole connector on the TCI module, that's just not connected to anything

 

If you are talking about the one in your hand? That would plug into the TCI that you have pictured.

 

There are four cables on the connector that plugs into the TCI, there are five blades on the TCI itself for the connector to potentially connect to

Meaning, there's a whole specific connection that is unused.

Is this TCI unit, reused on other models, and other models have something extra that they do, that the 650 doesn't?

 

Just the 4 wires in that connector to the TCI is correct.

 

That unused pin is ground as it connects to the pin across from it that has the black wire on the harness. Just a guess but it's left over from when some of the pickup coil assemblies used a two wire ground instead of a shared ground, so it would be needed to supply a ground to one pickup.

 

Exactly right!

 

I updated the bike to have this fuse box, however, in the position you can see here in the photo, I can't actually put the seat back on, it is too far forward, even though I used the template that was given. The risers (seen in photo) don't see to help, the only way I would be able to put the seat on would be to shave down the plastic on the underside of the tab on the front of the seat.

More importantly, the bike starts, and the bike runs. I let my girlfriend, who has more motorcycle riding experience, ride the bike a little bit, and it was unexpectedly stalling even for her.

When this happens the battery was about, 11 something volts? And we had to wait like 30 seconds for the battery voltage to creep up a little bit, and then we started it again and then it worked. This made the battery dip quite a bit and I think it actually started even with the multimeter reading about 10v point something. Once the bike was started again, then we were seeing a charge across the terminals of around 13 and more as we revved it up.

I'm not sure what else to check here, should I just instead get a AGM battery instead of lead? Should I replace the brushes and clean the contact surface? My girlfriend was suggesting that maybe the carbs needed to be resynced? I didn't get the chance to adjust the idle screw, but that can't be everything. The reason that she was saying that the carbs need to be resynced, because it seemed to her like when it was going from a high RPM to suddenly going to a lower RPM when coming to a stop, it's like the engine is starved, and then stalls.

And of course, as these things are, once we parked the bike last night, we noticed that the front forks were leaking. Which is very frustrating. The guy said that he already worked on those!

 

If the battery is discharging then the charging system is at fault.

Regulator
Generator
And all the connections between

The connections are known to melt from the generator and regulators are known to fail.
Brushes are the main issue with the generator.

If the brushes look good and the connections are great then replace the regulator. If it's not that then at least you know it's one of the other 2.

 

I looked at the cable connections on the regulator and they all seem to be fine. I didn't see any damage, so I'll order some brushes. I already have some crocus cloth.

 

After you get it sorted then you can move onto the sync and the forks and the... These are pretty old bikes.
Pretty solid too but maintenance is key.

Connections were a big issue for me on both of mine.
I have gone through and replaced most of the original plugs with Deutsch plugs while in a fit of overkill.

The trick with water ingress into the harness is to hold the terminal on the end of the wire with one hand and pull on the wire with the other hand as the insulation is sometimes the only thing actually keeping the terminal attached to the wire and the copper has corroded away inside. It'll snap off or be springy if so.

At any rate, think of it as an adventure!

 

Previous testing indicates the charging system is fine. The first case with a fully charged battery and the second with a depleted battery. There is not a good timeline on the most recent event but it appears either the battery is bad or maybe there is excessive load? Are there any non stock accessories added? Is the headlight stock 55W?

Does the battery maintain its voltage overnight? Do you have it on a maintenance charger?

 

The last time that I had had this problem on my own, about a week ago, granted I didn't have my multimeter on me at the time, the bike wouldn't start after having just rode it an hour and a half before. Based on previous behavior, I'm assuming that the battery was too discharged to start.

About a week or so after just sitting in the parking lot, when I touched it Saturday, it started up immediately and the charge was fine on its own.

I don't have it on a maintenance charger because I don't have a garage and it's parked in my apartment complex's parking lot. The only way that I am going to plug it into a maintenance charger, is when I bring it to my girlfriend's, during the winter.

I think it's pretty much stock, other than a Gemini exhaust, some replacement mirrors, and maybe the front brake/clutch levers on the handlebar.

I do not know the wattage right now of the headlamp, but I do plan on replacing it soon, with an LED headlamp. One person on Reddit gave me a suggestion for a headlamp that should just fit right into the housing.

 

All sounds good for the battery there, so as cds1984 suggested there might be a poor connection somewhere and in this case an intermittent connection that disables the charging system. I guess I would try getting a meter attached so the battery voltage could be monitored while doing a test ride just to see what is happening.

Replacing the brushes and cleaning the field coil copper rings is a good idea with these old bikes as Yamaha suggested brushes be replaced at 10.000 mile intervals - although I suspect not many do this.

Is it both sides? Is there any pitting in the usable travel range?

 

I'm not sure how to answer the second question, but it seemed both forks were leaking. We had parked the bike and then looked at the tire and noticed it was wet, and we ran our hands over the fork, and the left one was oily (more) but the right was also oily (less)

 

Sometimes with older bikes especially if stored outside and not used the fork tubes become pitted from rust. The fork seals just can't tolerate the small holes and even with new seals they are likely to leak fork oil.

 

If the forks are pitted, I can check tomorrow, does that mean I have to replace both of the forks?

 

I have never tried it but it is supposed to be possible to fill the holes with epoxy and sand smooth. I don't think that is considered a long lasting fix but something to get by for a while. Let's hope they are not pitted and maybe there are other options like cleaning the seals. Hopefully, someone on here has tried the epoxy if that is what it needs and they will add to the story.

Maybe you could reach out to him and ask just what he did - like did he install new seals and replace the fork oil after a good clean? Most PO's would be interested in keeping their old bike going for the new owner - if he's a flipper he might tell you anything to get the sell. Don't let that get you down though, I feel like I have been walking around lately with "sucker" tattooed on my forehead.

 

It wasn't that, the PO was my now passed grandfather, and my dad sold it to my grandfather, before that, and now it's mine.

"The guy" in this case was the mechanic I paid to get the bike running again.

 

Looking at your bike photos above, hard to see the forks, but the fender and headlight stay don't look heavily pitted. Likely you can just scrub the minor fork rust with some 0000 steel wool and smooth them up. Might not be perfect, but "good enough" is often the answer on a 40+ year old bike.