IIRC OP stated this all started when he replaced his single field wire alternator. Perhaps the OP should try another alternator?
the VR101 is (and Im 99% sure of this) an all electrical voltage regulator housed in a electro-mechanical style housing. the only way to "blow them would be to short the output to the alternator. (as others have said) the alt has a short in the field coil but it is intermittent that would explain the symptoms.
you can completely bypass the electrical wiring in your car by removing the field and heavy supply wires off the alternator, removing both the wires off the voltage regulator and running some jumpers.
run a jumper from one field wire of your 2 field wire alt to battery negative
run a jumper from the VR case to battery negative
run a jumper from alt case (housing) to battery negative
run a jumper from alt output ( heavy wire /Large lug) to the battery Plus
run a jumper from battery plus to the ignition side of the VR.
Run a jumper from VR field to the other field wire of your 2 wire field alt
start engine and see what you get at the battery.
@Mattax would you review my logic!
this is how I would start to be sure the alt and VR are working correctly, then I would start tracing wires and see if there are any with cuts to the insulation, kinks that might have resulted in broken strands, melted areas where wires could be touching etc
Side note about melted wires. along time ago I worked for an office building doing Fac Operations. we had a outdoor cooling tower that kept blowing its cir barker.
i noticed that it only happened a day after it rained. so I convinced the engineer to look at the wires in the metal conduit near where someone had been doing some welding. sure enough the wires inside had been heated enough to cause the entire group to be melted together and sure enough that day it was the day after a rain and sure enough the wires were wet.
moral to the story... it can happen!
