Charging System Question

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 ?
This is all 100% stock 63 wiring. No fusible links. No "direct wire" to the alternator. It's all stock. Big red runs from the alternator through the bulkhead, to the ammeter, back out the black and "wherever" it goes from there......evidently to the battery. It's not bypassing the ammeter.....it's not charging. Period. I put the meter both directly on the alternator and the battery as well. It shows battery voltage only.