Alternator/charging questions

It's possible that you have an interaction (electrical interferance) from the msd.

It's also possible that you have a bad rotor. When rebuilders get ahold of these alternators, several things can happen

1 Rotors may be mixed into the wrong application. Please don't ask me what all the combinations are, don't know. I do know that some rotors are different. The round back rotors surely are different than square back, at the very least

2 Rotors (and even stators) can develop shorts such as a few shorted turns, and be difficult to run down. What this causes is for the rotor to develop less magnetism while drawing too much current. It also lowers efficiency, and causes heating, which might explain the diode failure.

Other than that, the only thing I can suggest is start over with a "known good" unit.