Glad you found your main issue, I'm sorry if I didn't address all of your questions. You do not need to remove the butterflies to replace the seals but it sure makes the job easier.
As for your 11.5v reading, what does that same meter say when you measure a new 9v battery? I've seen a few instances where a meter reads incorrectly and gives a false impression of the circuit under test. Make sure you are reading with a good meter. If you still have low voltage after this, you really need to check your alternator brushes first. low/bad brushes will burn out batteries and cause a host of other little nasties so I'd check them sooner rather than later.
JB is good for some things and this may be one of them. It all depends upon surface prep, cleanliness and temperature. Lower on the exhaust means lower temps so you may be ok. Given that you cannot get a good seal inside of the leak, your fix may only give a short reprieve before it comes back so plan on a more permanent fix.
Best of luck!

thanks for responding, robert.

that's a good tip about the voltmeter possibly being inaccurate - i'll double check it with my older analog one.

i already checked my brushes and i believe they have lots of life left. there was a mark on the brush (kinda looked like someone pressed their thumbnail into it really hard) and not quite a 1/2" of brush beyond that. i was under the impression that the line is the wear mark and as long as you've got *something* past the mark, you should be ok.

i've got a feeling they've been replaced by a previous owner because the alternator cover screws were allen head screws and not the "screws that look like philips head screws but aren't" that RickOMatic mentioned in his "check thine brushes" post.

however, i am wondering if i messed something up when i checked in there - the cover kinda fought me going back on - it didn't seem to want to line up quite right. i chalked it up to all the magnetic stuff in there pushing me around so to speak. think there's something wrong in there?

assuming the meter is correct, it is definitely a charging issue and not the battery, right? i'm assuming that even if a had a bad battery, the voltage would read whatever the bike is supplying regardless of what kind of shape the battery is in?

also, would it be a safe bet that if there's low voltage across the battery and the brushes are ok, it's most likely a)a bad ground or b)a bad voltage regulator?

The line on the brushes is the limit line. If you have plenty of brush past them, you should be in good shape.
Replacing the cover can be a dicey affair, I can't say it is one of my favorite things to do either. I've fought the same fight as you so I know exactly what you are referring to. You do need to be sure that you slip it on square. It can, and sometimes does, slip on cockeyed so be wary. You are fighting the brush tension and the stator ring. It helps to have some idea of the alignment of the cover before you try to juggle all the parts into place. By this I mean ensuring that the stator is properly pressed into place at the right alignment (it is loose and will shift if you aren't on the ball). The other players in this act are the alternator wires and the seal that they pass through. That seal is hard as a rock by now and it doesn't like to flex very much so this can be a problem too. I recall juggling the seal, one screw, the stator and an allen wrench while trying to line it all up. Man I just don't like fussing with that cover.
As for the voltage, if the voltage is low and you don't see any voltage increase at 4-5Krpm, you do have a charging issue. This does not mean that the battery is safe/good but it can be a good indication as to why it may not be happy anymore. Do you have a maintenance manual yet? If not, you NEED one. It is the best tool you will ever own for your bike. The Haynes has a section on how to test your alternator and so on. I've the factory manual for your bike (available on the XJCD, well worth $10) should you need further assistance.
You can have the battery load tested to determine if it is sound or not.
Most likely is a grounding issue but a bad voltage regulator isn't out of the question. Go through the bike and clean all of the ground connections (back of the engine case, next to the coils, near the voltage regulator, etc...) and see if that buys you anything. It's free and will eliminate one more item on your to-do list.
Good luck!

well, i was feeling a little inspired after work this morning, so i decided to take a look-see.

i did a bunch of voltage checks on the battery and they were as follows:

on the battery tender: 13.42V
off the battery tender: 13.36V
ignition on: 11.57V
cranking the engine: 9.2V
running at idle: 11.49V (running with choke at ~1400RPM)
rev'ed up: 11.57V (assuming the tach is accurate, ~4000 RPM)

i also checked battery grounding as follows:
from the battery negative terminal to . . .
. . . brake pedal: 0.4 ohms
. . . ground wire on ignition coil: 0 ohms
. . . bare* spot on valve cover screw: 0 ohms


* the previous owner painted the engine black, but much of the paint is coming off, so i found a "bare" spot on the screw if ya catch my drift.

i know i checked the charging system out last summer, but unfortunately i didn't take any notes and i was hoping i posted something about it here, but can't find that either. i *can* tell you i took several 200+ mile trips without the battery dying and giving me problems.

do these numbers look alright?

did i bugger something up with the alternator cover?

did something go to sh*t on me?

any input is appreciated.

Good check on the ground system, that should let you breath a little easier. You still need to check the resistance to the ground wire on the voltage regulator. I am a bit concerned about your alternator output. I don't see how you can damage anything installing the alternator cover but it sounds like you do have a voltage regulator that is bad. They pop up on flea-bay regularly so a replacement shouldn't be a problem to find cheap. Source one and see what that changes. If no change, your charging system would be the next step given your alternator brushes check out. Oh, and I wouldn't take the bike out for more than a few miles ride until you get this sorted out.

Robert wrote:

You still need to check the resistance to the ground wire on the voltage regulator.

can you be a little more specific here? i'm guessing my voltage regulator is the thing on the left side of the bike with a big heat sink on it, right? resistance between where, exactly, should i check?

thanks

The black (B) wire is the ground. Yes, the regulator (2) has heatsink fins.

Thanks for the backup Markie! A picture is worth a thousand words.
If the regulator isn't seeing the same ground potential as the rest of the system (or various parts), it could well think that it is correctly regulating when in fact it isn't. You have to ensure everything sees the same ground potential so everybody plays nice together in the sandbox. Incidentally, I've a few spare regulators in my parts bin should you require one.

much obliged. i'll check it out in the next day or two.

Unplug and inspect the contacts in both sides of the big connector off the regulator; a common point of failure.

Another issue that has cropped up occasionally with alternators is the internal corrosion of the tiny braided wires coming off the brushes themselves. The brushes may have plenty of wear left, but if their little lead wires are all green inside they won't carry much current.

I think you need to pop the alternator cover off and do a careful inspection.

good news: the black wire going to my regulator shows 0 Ohms to the battery neg. terminal, so that ground is good.

bad news: there's a hole melted in the connector and the black wire came off the connector. i'm assuming the melting is due to the bad ground.

question: do you think i fried that connection using my battery tender while the battery is on the bike? (if i did make a mistake there, i'd at least like to learn from it, ya know?)

i figure i can get away with just cutting the ground wire off the other connector and and splice 'em together.

the other terminals all had a light green corrosion on them, so i'll clean them up, too.

it's kinda bittersweet finding out what's wrong, eh? it's a relief to know what the problem is, but, darn it, now you gotta fix something.

at least now i have enough experience with this bike to say "looks like i found A problem" instead of "looks like i found THE problem"

another question: are there any checks i can do to the regulator while it's disconnected to verify that the regulator itself should be performing properly?

well - i got done with work this morning and after attending to a few things, then i reinstalled the voltage regulator. i cut the ground wire off the connector and soldered a new "bullet" connector to the ground wire and plugged everything back in. i checked the new terminal and showed good ground, so i'm 99% sure my re-ground work is ok.

bike started up no problem. eagerly, even.

unfortunately, i only get 11.61 V across the battery no matter how high i rev the engine.

a couple minutes after i shut the bike off, it occurred to me to check if the regulator was getting hot. it felt warm to the touch, but definitely not HOT. not sure if it's relevant, but it's information none the less.

anyhow - based on the 11.6V, is it safe to assume the alternator is ok and all my problems lie within the regulator?

fitz- to check those lead wires, i'm assuming i should do a continuity check from the brushes to *somewhere*?

If you look at the diagram I posted, the brushes are not shown, but transfer the excitation current to the small coil shown next to the star shaped set of coils on the alternator (1). Hopefully, you have already measured that the 3 white wires are all connected together and not shorted to earth.

To do a quick test for continuity, unplug the regulator (2) -Ignition off- and test between the brown and green wires - you should get a circuit, although I am unsure of the resistance reading. The regulator works by varying the strength of the magnetic field on the rotor (Hence the need for brushes).

Fitz is suggesting that corroded wiring on these brushes could be the cause of your lack out output. You need to check them visually although your earlier post says you have.

Actually what Fitz is suggesting is that even though the brushes have a lot of "meat" left, the little braided wires could be green inside.

It takes careful visual inspection (with a magnifying glass if necessary,) and "flexing" the little braids to see if they are corroded green inside.

It's a condition that's not always readily noticeable.

Mark is very sorry!