1994 fourtrax stator/rotor issues

I have a friend's fourtrax after he "worked" on it. He had reversed some wires replacing the starter and caused a multitude of problems. Essentially everything had been replaced after, short of the stator and pulse coil. I ran through all the wiring to verify it was correct, followed the service manual to the letter and cam up with low voltage on the sense wire, as well as the pulse coil not giving the proper voltage to the CDI. I replaced the stator and pulse coil, and it ran for about 10 seconds. Couldn't get it to restart, and the voltage checks on the pulse wire was still good, but the sense wire was low (around 1.2 volt when manual says 3 minimum cranking). Checked for other problems and found the regulator/rectifier had some questionable checks on diodes. Replaced that and the stator again and did the voltage testing prior to connecting to the regulator or the CDI, and the voltage was low when cranking. It appears that the magnets in the rotor are strong and evenly spaced, the gaps are exactly the same from one stator to the next. Engine is cranking at an adequate rpm. Surely I haven't gotten two bad stators that test fine on resistance checks but put up low voltage. I can put 3vac to ground on the sense pin from a test set and it starts and runs, but not enough voltage to run on its own even at higher rpm. Is it possible the flywheel/rotor is bad even though it seems fine?