Don't do that! Just jumper the VR to bypass it if you think its the culprit. Same idea ias dadsbee wrote but just answering the question if its a regulator problem.
Exactly could have burned one of the fusible links in there.
I think this is your answer.
With a wire going directly from the alternator to the battery, the ammeter doesn't see charging current.
As far as more discharging while running, apparently the easiest path to the main splice is to go to the battery first.
Is there also a wire from the alternator Batt terminal through the bulkhead to the main splice ?