when you followed with all this stuff (then the cdi,killswitch,ignition,coils) did you mean you swapped that stuff also. if so maybee some wires are not correct? i had the one cylinder prob a long time ago but it was just a bad plug. 2 brand new plugs and i was movin again. was it a stock stator? did you ohm the plug wires? hhmmm hard to just tell you i am better at hands on.
go with that and see what happens.