Hammer, back in the Late 70's I was working in a M/C shop and had a 400 Honda that had a mis fire that we could not track down.
There was the exact same second hand bike in the show room so I bought that out to the work shop and systematically started swapping parts.
Starting with the easiest things first.
First I swapped the carbs over, this made no difference so left the swapped ones in place, next was the spark plugs, again no difference so didn't swap them back, next the coils etc etc.
In the end it turned out to be the rectifier which was hard wired into the Alternator.
My point is, you have done a lot of work so possibly you should start swapping components with a known good bike.
I would start with the starter motor.