If I was troubleshooting this at this point, I'd check the field current while the engine is running and also the output voltage, as well as the field voltage. A look at those 3 things should point to the failure point. Along with repeated ohm meter readings of all the windings and checking for shorts to ground it should become obvious what is wrong. Every once in a while I've found bizarre things that I'd never suspect though
! One time I scraped the lighting coil on a Suzuki 250 using the wrong puller on the flywheel and then the engine had a miss when the headlight was on. Two of the outer windings were a little flattened but the coil measured perfedt electrically. Replaced the coil and spark miss was gone so I'm guessing that the shape of the magnetic field was somehow altered or weakened by the shape of the wire being changed. It didn't seem like the winding was shorted or anything, just flattened from round a little.
Truth is stranger than fiction... Leland