82 Maxim 650 Carb Issues; Dead Cylinder

Hello all, thanks for checking this out. I have an 82 XJ650 Maxim, stock exhaust, deleted airbox with pods & stage 2 dyno jet kit installed by previous owner, I believe it to be the "J" model from the vin and case number searches I've done, however I have newly discovered the carbs are out of an earlier model due to the mixture screws having a coarser thread pitch rather than the ultra-fine. I don't believe that is terribly important to the situation, but still.
For background, I started having issues with the bikes running condition to a point that I needed to replace the throttle shaft seals. Did that with the v-seals from chacal, I used some silicone grease (I believe on all of them) and made sure the opening of the V was on the outside of the carb. the only concern that happened during that was one of the middle carbs (with the threads and nut to secure it) was extremely hard to remove, to a point where it was forced out, I remember looking and seeing that the surface it went across looked fine and not scarred, but I'm unsure if that could've gauged the hole just big enough to not seal. However, I'm not even positive that happened on the cyl. 2 carb so it could not even matter. Regardless with it being my first time fully tearing down the carbs, I had to fight with it a few times to do it right.
I have now gotten them to a point where the bike sounds to run great, but only on 3 cylinders, No.2 does not fire on its own. I have the mixtures currently set at 2 turns out (should be 3.5 according to dyno jet, I was just curious what this would do, and it seems to run good with the misfire, so I haven't changed it till I get my vacuum gauge back). My idle screw seems to be backed all the way out, maybe slightly touching. I found the dead cylinder simply from feeling the headers after getting warm. I've checked compression, spark, new plugs, float height, jets, cleaned many times, replaced all of the intake boots to the engine. I may be forgetting others, but I believe I've checked everything that would cause the dead cylinder in 1 of the 4, especially 1 in the middle of 4 carbs.
I put some gas in a spray bottle and sprayed into the intake, and it revs up (not high, hits 2k tops with current settings) and seems to be firing in cyl.2 as it should be, though I haven't put the vacuum gauges to it at this moment. I have also noticed the same result if I put my hand mostly over the intake opening, unsure if this is because I am covering the 3 airports too much or because of an air leak in the carb itself (Figuring said throttle seal.) I was watching the temp with my heat gun and could see the temp on the 2nd header raise and drop with my hand being taken on and off of it.

Considering that all, does it sound like my theory of the new V-seal leaking sound correct before I rip it all apart again, or is there something I could be missing? Also is there some special method to installing those seals that I could've missed besides having it face outwards, sitting flush and lubed? Also, how should I be setting my Idle screw, especially when trying to start it after a rebuild, I kind of know how to find it when it's been running but is there a suggested starting setting?
I know it took a long time to get to the actual question, but I hope the explanation was somewhat helpful. I appreciate anyone who at least read through it, sorry if it's confusing or a ramble, this thing has been kicking my buns.
Please ask questions, it's very possible I've left out something, phrased something wrong, or am just plain dumb. Any help is appreciated. Thank you

 

Get the vacuum gauges on it and see what's actually happening.
It's fairly common for it to run like a bag of spuds, with one cylinder not even working right, because everything's a mile out of sync.

 

Thanks for the response. I finally got my tool back and motivation to see what I could find.
I think it's a good thing, I waited to get parts because the vacuum test seemed to check out, at least in the sense that they are all even in their readings. However, my vacuum gauge is the Digi sync (pretty nice, no noticed issues atp) it reads vacuum in numbers, I am not sure what the numbers for the vacuum actually represent in relation to RPM. Also made sure to check numbers with the YICS tool in, though it was not at operating temp, only ran for like 1-2 min before putting it in.
If I'm correct that gauge would only be reading how much air its pulling, not if the fuel and air are being mixed enough; I would be right to assume I do not have air leaks...right?
If so, I have spark, air, compression, timing checked and valve clearance checked. I've cleaned and reverified that everything is correct inside the carb so many times, but it makes me think the only other option is fuel issues.
Also, at one point of running it, I tried covering the intake for No. 2 to see if anything happened, nothing actually did until I put my finger over the top large center duct (I believe it goes to the slider cap area.) Right when I covered it, rpm went from about 1.3k to 4k and held there for a little, even after taking my finger away. This could be total normal and hopefully I didn't screw it up further cause it randomly punch out a bunch of air from that port (cause I restricted the slider?) and made me think that N0.2 starts firing while its idling around 4k. I know at the least when I sprayed gas into it and covered it on the previous time running it, when I touched the 2nd header, I could feel it getting hotter and hotter, enough that I'm pretty confident it was not just from the other headers radiating heat onto it.
I know a lot of this is rambling but it's the only way I can really get all my concerns and ideas out without making a ton of replies.

Thank you again for the response, I hope I explained it understandably.

 

Couple things.

First: "idle screw seems to be backed all the way out, maybe slightly touching." If the screw is all the way out or just barely touching, then the throttle plates should be completely closed but for whatever is set via the carb-to-carb linkage. The idle screw should be pressing against the throttle linkage, at least a little.

Second: if it was idling badly enough to require new throttle shaft seals, then you fixed at least one vacuum leak, and that's going to affect how much air goes through each carb (reducing the amount on the leaky carbs), which in turn means you need to re-synchronize them. I know that after I rebuilt my carbs a year or so ago (part of reviving a bike that had been stored for twenty years with gas in the carbs), it ran horribly until I hooked up the vacuum gauges and found the carbs so far out of sync that #1 was completely shut off at idle.

I am trying to make sense of "I put my finger over the top large center duct (I believe it goes to the slider cap area.) Right when I covered it, rpm went from about 1.3k to 4k and held there". I thought that passage went to the chamber under the diaphragm, and the lower pressure in the venturi (passing up through the hole in the slide to the chamber above the diaphragm) is what lifts the piston... so covering that port shouldn't cause the engine to speed up. But I don't have the manual in front of me, so I might have the wrong port in mind. Did you notice the slide moving any?

My (mechanical) carb sync vacuum gauges have a helpful (not!) sticker saying what various numbers might mean. Worthless. I will say that on my 1980 XJ650, it sits around 5-ish inches of water vacuum. This is much less than the sticker (which, I suspect, is calibrated for a car) says is "correct," but I work on the assumption that the only meaningful thing is that they are all the same.

 

1. Get a good sync guage. My preferred is the Morgan Carbtune Pro. It sounds like you have a carb so out of sync that the butterfly is closing so early that it’s holding all the others open.
2. Get a colortune plug. That will help you get mixture screws set. I don’t care what dyna says, or Yamaha says, past their recommended setting….. it’s an INITIAL SETTING. A STARTING POINT. YOU have to DIAL IT IN FROM THERE.

3. If you think a throttle shaft seal is torn, spray some ether or unlit propane torch around it. If the engine revs right there, yup. If it doesn’t, then it’s fine.