'89 FJ1200 missing #1 cylinder at startup, sometimes while running

[aigram]

I have a 1989 FJ1200 that seems to be intermittently missing firing off the #1 cylinder at startup. When this occurs, at idle I can put a hand on the #1 cylinder exhaust header and feel no heat or pulse. With revs, the cylinder begins to fire off and idles perfectly. Sometimes though, after the bike has warmed up, I can notice the cylinder begin to miss again. I also notice gas coming out of the left side carb overflow hose when this happens (1 of the 2 larger hoses, those are vent tubes, right..?).
Recently went through and inspected/cleaned the carbs. I also used the 121 piece screw and o-rings carb kit from RPM. I did not replace the fuel transfer tube o-rings, or the idle mixture screw o-rings; these appeared to be in good shape, but I'm bearing this in mind as a possible culprit.

I have done this:
Cleaned carbs, used 121 piece kit, EXCEPT for the o-rings for idle and fuel transfer
New plugs
Cleaned plugs
Checked plug gap
Swapped #1 and #4 plug. Problem stayed with #1 cylinder

Thoughts on what is going on here?
In summary, when all four are firing I notice no gas leakage, no rough idle, runs as expected. When #1 is for sure missing, I notice gas out the vent tube, rough idle (duh) and poor acceleration. I'm verifying that #1 is not firing when bike is cold by keeping a hand on #1 cylinder exhaust header. When bike is at operating temperature, I notice quite poor acceleration from standstill and am surmising that #1 is missing when this occurs.

[racerrad8]

I have done this:

Swapped #1 and #4 plug. Problem stayed with #1 cylinder

Did you switch the plug sires between 1 & 4?

If you do that and the problem goes to four then you have a bad plug wire or more likely spark plug boot.

Randy - RPM

[aigram]

Hey Randy, wouldn't the bike have quite a hard time starting, if #1 and #4 plug wires were swapped, changing their position in the firing order?

[racerrad8]

Hey Randy, wouldn't the bike have quite a hard time starting, if #1 and #4 plug wires were swapped, changing their position in the firing order?

Nope, the ignition system is a wasted spark system on one of the two spark plugs of each spark signal. One coil fires cylinders 1/4 and the other fires 2/3. Since there are only two coils, you can swap 1&4 to see if the problem moves.

Randy - RPM

[Millietant]

Presumably the same applies to the 2/3 coil- say if No 2 isn't firing, switching plug leads between 2 and 3 will help see if misfire switches to No 3, or not.

[aigram]

I resolved the rough running/missing a cylinder by pulling the carbs for a second time, cleaning everything again, polishing the needle and seats. Cylinder 1 spark plug reaked of gas.
Somewhat related, I also ditched the stock airbox in favor of UNI Pods, re-jetted according to Randy's recommendation, set the mixture screws to 3 turns out, synced the carbs, and now it runs great! I'm no pro at carb tuning, and I can tell there's a flat spot around 3500rpm, so I clearly have more tuning to do.