Okay, got it figured out I think. The last few days have caused somewhat of a headache, for various reasons.
What I ended up doing was going to single-phase, using three identical coils wired in parallel, mounted 120deg apart. Floating ground. I used the TrailTech regulator/rectifier: http://www.treatland.tv/trail-tech-DC-voltage-regulator-rectifier-150w-p/trail-tech-reg-rec-7004-rr150.htm
Seemed pretty straightforward to set up -- each of the two yellow wires go to each side of my bundle of three parallel coils, then black and red are 12VDC. However, when I first tested it, I was getting some weird operation -- maybe 6VDC at idle, then dropping down to 1VDC as I revved it up. Turns out you need a battery (or something else -- more on that later) to get the regulator to do anything. So, I hooked up a battery, and hooray, perfect operation. As long as the engine was spinning fast enough (about 3000rpm on my stator), it would make wonderful 14VDC for as high as you could rev it.
But, after a ride, I noticed it was being wonky. At idle, it was mostly okay, but as time went on, idle voltage diminished and it would get all crazy at high RPM and cut out (I have an analog needle voltage meter on the bike that is susceptible to bumps, but man, that needle would move like CRAZY!). Finally, today I realized the problem. While testing the AC voltage output from the coils, I noticed that it would intermittently cut out and the multimeter would reset. I peeked in the rotating flywheel, and as I revved it up I could see lots of green light coming from inside the flywheel. Oops. Pulled the stator off, and sure enough, some wires had desoldered themselves and were flapping around making sparks.
After repairing the stator, tried again, but still got erratic operation. Finally, I said "what the hell, throw a capacitor on it." So, cap from 12V to ground, fire it up, and YAYYYYY perfect 14VDC!! I have yet to ride around much, but it seems like as long as the stator doesn't fry again, it should be OK. Pretty sure my battery is killed, I rode it around and it was making beautiful 14VDC. At the start of the ride the battery was at about 11V, but the it was very dead when I shut off the bike at the end of the ride -- 5V. I confirmed after the ride that the battery is seeing 14V from idle and above. So I'll get a new battery and maybe everything will be okay from now on.
Anyway, now I can do fun stuff: