Too many noisy electrons will create issues. Not sure about the wiring change though. Battery to starter and wire from that same terminal to the regulator. How does that differ from a wire direct from the battery to the regulator? And what is the noise source? I don't know about electrical issues to pass judgement - just trying to understand and clear the smoke to see what is actually happening.
I get that the ignition might have some sort of thermal overload protection but it made no sense that the charging circuit was a cause of overheating. Good to see that theory has been taken off the table. Keeping in mind that I wouldn't know an electron if I ran it over, I wonder if that new alternator might be generating waves (ripples) in the DC circuits that caused the ignition to freak out. Maybe the new regulator acts as a smoothing device in some way.
BTW, most bikes now seem to have a 30 amp fuse built into the starter solenoid wiring between the battery and everything else. If it blows, all power to all circuits is cut, so no more engine generating power, so I'd guess that is not an issue.