No more than 12.5 charging-Has to be VR problem?

The voltage too low is an odd one. Just for grins did you double check voltage with a different multimeter with fresh batteries? For sanity it would be handy to swap your "bad" vrs with another car.

There are only a couple wires to make it work. Should be able to make a jumper harness 1 wire at a time. Once ruled out the most probable, the impossible becomes suspect. I would run a clean wire to the switched power on as well. Ground the alternator case to the VR case.

http://i1271.photobucket.com/albums...rnal_voltage_regulator_wiring_zps8df13fa4.jpg