Somewhere on Steel Soldiers, in the past two months or so, someone posted a huuuuuge file (multiple GBs, I believe) that is a pdf with every electrical tidbit ever discussed on SS, regarding the CUCV. I have it saved if you need me to email it to you; I tried posting it here but it is too large. That may hold the key.
Personally, I wonder if you blew a reverse polarity diode somewhere. They tend to be horizontal black cylinders, not tapered in the middle like a resistor, rather strictly cylindrical in shape, and not vertical like a capacitor. Worth a guess...my two pennies for the day.
EDIT TO ADD: A quick search of that pdf reveals no mention of a reverse polarity diode...however...perhaps the alternator literature would be that specific.
EDIT again because I had time to kill...here is a link to that document:
http://www.steelsoldiers.com/showthread.php?163054-CUCV-Electrical-PDF