I went to start the bike the day after getting it all back together and found the battery dead. I charged it and put it back in and did a little meter checking, suspecting a parasitic drain with the key off. No such luck. Zero drain with the key off. I switched the meter to volts and started the engine. Instead of the voltage rising slightly when the engine was revved, the voltage went DOWN! I did the test several times to make sure I wasn't imagining things, and the problem is real. The funny thing is that the voltage dips anywhere from two tenths of a volt to 5 or 6 volts! Something is intermittently creating a massive draw when the engine is running.
First suspicion of course is the rectifier/regulator, so I ordered a new one on eBay. It's cheap enough that even if this isn't the problem it will be worth it to just have a spare on hand. The only other possibility I can think of is some weird shorting going on in the stator coils.
So I'm just putting this out there in case someone else has run into, or heard of, this kind of problem before.