You should verify all grounds are good and in the factory location. Also, make sure the engine is grounded to the frame, if you had the frame painted...
For the stator differences, they are different, stator + flywheel does swap as a set, and the 86 style is the upgrade so would be ideal to keep that....
Sadly the source we had for the round 6 pin CDI connector stopped offering them. Could ask Mike (Oscarmayer) if he has any adapters left though. Not...