I think your main problem is a the flywheel.If you don't have the proper key in the keyway,the flywheel will move when the bike is running causing the erratic behavior you describe.How did you remove the flywheel? Did you have the proper puller,so the flywheel didn't get twisted.What the problem with the starter drive that keeps popping up? If the grove in the flywheel is wore,or the flywheel is not seating on the crank properly, that will alter the timing enough to cause your problem.
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