I had an identical problem that persisted for 2 years, regardless of carbs, jetting, even different cylinders. I was convined that the problem was jetting at first, then figured it was electrical. Swapped CDI boxes, ignition coils, but not stator. It didn't act like a stator issue. I bought an '06 and put the same top end, carbs, etc on it and it ran great...no sputtering, etc. (I did however seize the mf'er up by setting for about 15 mins and letting it cool off accidently in 30 degree weather, then hauling ass on it............cold seize.)
But my problem was exactly like yours,....only ran like piss at WOT, regardless or lean or rich condition. I have changed the stator and will know tommorrow if it fixes mine, but I'm pessimistic.