Alt volts
Chief was correct, except that the problem wasn't at the bulkhead. I did the MAD bypass a while ago, and my shotty soldering is to blame. Turned out the circuit had an open spot. Since the vreg was telling the alternator that the battery was low, the alternator would increase its output but to no avail.
Sadly, the alternator seems to have cooked itself. After I fixed the bad connection, the alternator pretty much wasn't doing anything at all. Only 12.4 volts output when hooked up to the battery. I picked up a new alternator and got 14.7v at the alt, 14.5 at the battery. That's as good as I've ever had it.