Hi Brian. Just recapped message #346. Are you running a single carb? There is an odd comment that suggests you "swap carbs".. but I assumed this was one on the engine swapped with another on the bench.. But if I have missed something and you are on twin carbs, it may be the carbs not the ignition causing the different running on the 2 cylinders.
Anyhow . Considering your mis-fire or non-firing of one cylinder, on a V-twin with common carburettor the intake manifold be sensitive to fuel distribution, due to the timing difference between left to right and right to left intake opening separation intervals.
Even with twin carbs, my V-twin motorcycle is the devil to balance at idle, and just off idle. As it has a tachometer, it is necessary to pop the plug on one cylinder, set the idle on the other as a single, then do the opposite for the other carb. Then when both are connected and running, or mis-firing, I need to fiddle further to get some stability as with 2 cylinders running, the idle is too fast from setting as a pair of singles, and the off-beat of the Vee-twin means one cylinder always runs sweeter than t'other.
So, if you are running a single carb, when tuned right for the best cylinder, it won't run without misfires on the weaker cylinder - if like my bike - so instead you need to set the weaker cylinder at its best, and accept the better cylinder won't be perfectly tuned.
Anyhow, that's my experience of a vee-twin tuning.
K2