can't seem to get the fueling right...

Hey all,
I know not everyone is signing up for reading a short story when they click on the thread link, so I'll try to keep this brief. I want to give important historical context, though, so here it goes...

I have a '82 Seca 650. I've had it for 11 years and over that time have taken the carbs out every 2-3 years to clean them out. My bike was running great until the timing-chain tensioner broke on me while driving. It was one of those times that I think to myself "the valvetrain sounds noisier than I remember it being before..." but otherwise everything seems as it should, so I didn't stop and check it out, and didn't what was wrong until i pulled into my garage and noticed the trail of motor oil down my driveway and down the street. I don't know when the even happened, but I noticed the timing chain noise less than a minute before pulling into my garage.

I pulled the cams off, checked shims, set the timing chain according to the procedure in the supplemental manual, replaced the tensioner, changed the oil+filter, and the bike doesn't run quite right. I check cam-sprocket alignment again, put it all back together again, and same story. While checking cam-shim clearances, I couldn't get half of the shims out of their buckets--I was bending all my stuff trying them out so I just left them as was without knowing their numbers. The ones I got out were either perfect, or only barely off by 1 increment of shim size(feeling lazy and not wanting to go find the spreadsheet with all the numbers)

It's been a couple years since the last carb cleaning so I get to it, wrestle them back into the bike and adjust the pilot valves with the help of my Gunson Colortune plug. The bike sounds great and revs smoothly while I've got it on the kickstand but the next time I start it from cold, it does a stumble-start and runs like I'm only on 3 cylinders.

Some drama later including a carb rebuild (not just a clean), syncing carbs with a manometer, compression testing (nothing of concern was found), dialing-in float height, replacing the petcock diaphragm, a new petcock vacuuum hose, new fuel hose, new fuel in the tank, and the carbs are back on the bike again. Another pilot-screw tune-up with the Gunson Colortune and it feels great!
A cold-start later, and it doesn't...

A few observations about the current state:

• The bike doesn't roar to life like it used to when started--it stumbles to idle but maintains idle fine.
• It is rough and weak when driving, like it's running on 3/4 cylinders.
  
• If I choke it while driving, I get the last cylinder participating again. As long as it's choked, it feels good.
  
• To find out which cylinder might not be firing, I put a thermal camera (Flir One) on the exhaust pipes coming off the head. These are my findings:

1. Cylinders 3 and 4 are basically the same temp and lower than cylinders 1 and 2.
   
2. Cylinder 2 is much hotter than everything else--like 100degC hotter. But it's tune is awesome according to the colortune.

• I ruled out bad coils by a resistance check.

• I swapped the coil lead from the left side of the engine to the right (can do this thanks to the wasted-spark system) and the temperatures don't follow the leads--they stay with the cylinders

I'm feeling like every road I go down with this is a dead end.

Do I need to adjust the main jets? I've never changed them before; never had to.