@Dave
The problem is that it doesn't give a spark...at all! The bike went fine after installing the new flywheel, then just died. No spark since.

I've refitted the flywheel a couple of times when switching between the two I have, wich is a bit tricky, but I think I got it right now.

If I should sum up all my problems into one question it would be:

Should the bike run (give spark) even if the side stand is down and the switch indicator says the biks is in 3rd gear (or any other but neutral)?

Why this is the "main" question is since I've tried with everything else as far as I know. And by that I mean removing components that I think might be broken causing no spark and refitting spares that should work.

Also, I should probably say that all other electricity works fine, the RC-servo motor, lights, incoming signals to PGM from pulse generator, sidestand, switch indicator (witch might be broken and send wrong signals..)
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MC21, GP-Replica (Daijiro Kato, Telefonica Movistar Team 2001)