Which Windings on Stator go bad

I have had this running problem for awhile now. Doesn't have the acceleration it used to and surges if you hold one throttle position. It occasionally fouls a plug for no reason. Just feels like timing is retarded all the time. I have lab scoped all the sensor inputs including TPS at the ECU while running and checked them with an ohm meter. They are all good according to manual specs. Pulled engine to strip down for inspection and checked out stator yesterday. All the resistance checks are within spec except for the AC charge coils. Resistance between coils is good but I get 5 Mega ohms resistance between coils and ground. Manual calls for no continuity between coils and ground so I am inclined to fail it. Not sure if you would get any AC ripple through the DC side with this condition. Looking for other peoples experience with bad stators and what actually failed. Driving me nuts so any opinions appreciated.

Thanks for the reply.
My mistake. It's Mega ohms. That's what bugging me. If it was milli ohms I would just replace.

Guess a little background is in order.
Its an 06 with 1100 miles on it. It was almost new when I got it but had been overheated and needed a top-end. I did that, installed all the SLP mods plus all the suggested mods on SnoWest like helix, gearing, weights, rad delete, oil cable etc. Ran great with no problems. Then I installed a Boondocker tuner and Racepac EGTs. Never got a chance to adjust anything. That's when problem first appeared. I removed them thinking there might be some feedback through TPS or injector circuits. Who knows, but you have to back up. Problem still there. I haven't rode alot the last 3 seasons but it is progressively getting worse. Last year I replaced intake boots, exhaust valve bellows, checked sensors and replaced exhaust temp sensor only because it's hard to test accurately. TPS looks good on a lab scope. Still no joy.
I've had sleds since being a kid and an Auto tech for almost 30 years so I know my way around fuel injection pretty good. The only question I can't answer is the above stator reading. I even tried 2 ohm meters just to be sure. Kind of hoping someone else might have run into same readings and could enlighten me. Charge voltage is fine.