After all that you replaced I would say bad stator. You don't need a flywheel puller for that motor,it bolts on. Check the stator for burnt coils or leaking potting. A sure sign of a bad stator,if stator looks good do a peak reading voltage check. You may want to go to CDI electronics website and check the trouble shooting for that motor. These igntions can be tricky to diagnose. Make sure the spark plug wires are gray factory wires and proper plugs QL78YC champion I think. They are the only ones that will work with optical ignition.
Have you tried disconnecting the temp sensors in the heads, they have had problems with them, and make sure they are not routed close to the spark plug wires.
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