High Voltage

Just a suggestion: I would not ever use a MaxiFuse in a power circuit like that which is subjected to large currents and the moisture of auto use; it would be Ok for temp use for troubleshooting but not for permanent installation. A MegaFuse and holder is all I would consider.
[ame]http://www.littelfuse.com/~/media/automotive/datasheets/fuses/passenger-car-and-commercial-vehicle/bolt-down-fuses/littelfuse_mega_datasheet.pdf[/ame]

Yes, the VR case is the ground. Sounds like it ought to have a good ground with your extra wire.

How hard wuld it be to move the alternaotr main output lead from the battery to the starter relay's big lug? There was a case here in the last few months where the poser had erratic charging voltage, and it all settled down when he moved the alternator wire to the starter's big lug. It gets it a bit closer to the VR.

And I agree with Bill's comment: the VR should be set so that it will put put proper voltage when the voltage between it's blue wire power input and it's case is around 13.5-13.8v. You have higher voltage (IF there are no ground circuit voltage drops), and yet the voltage is not regulated properly.