Nothing like a problem that moves around on you
You have any hair left?
Anyway, with the charge rate changing on you, it sounds like a grounding issue, loose connection, or a bad wire. I would first go over the engine to firewall ground connection AND the battery to frame connection (I know, again) just to be sure. Then make sure the VR (was it swapped out? if not it would be a good idea) is well grounded to the firewall. Then I would check the VR connector to make sure both wires are getting good solid contact to the VR. Then I would follow the two F wires from the alt to the VR. The blue one will come to a 5 way junction, the green will go straight from the alt to the VR. Check the insulation for cracks, signs of too much heat, discolouration, etc...
I would also check the newer wire from the alt to the start relay. The start relay isn't very big and sometimes the connections on the stud get a little crowded and loosen up/corrode on you. Just make sure they are tight and clean.
I've been looking into moving to Australia in the next year or two (3?), hopefully this gets solved before I get there.