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Update: Still giving me fits. I ordered a new rectifier/regulator today. After completely rewiring everything from the handlebar switch plug back, I don't know what else it could be. With the way it's set up, I can run the engine and not have any connections to the lighting coils hooked up. They are independent from the ignition system on the stator. I did ohms checks for the stator on each phase and they check out ok. I also "checked" the R/R but there's no true way to tell whether it's completely shot by just the resistance readings... which were a little different, which is suspect. What I do know is that with the way I have my lighting connected, I can independently unplug either the battery from the system, the stator from the system or both. With the fully charged battery(13.64vdc) connected and the stator disconnected, everything works exactly how it's supposed to. If I crank up the bike and connect the stator, it drops to 9.4 volts. With the stator disconnected from the lighting system, I can start the bike and measure the output of each phase of the stator. At idle, I have about 11.5VDC on each side. If I set the throttle at a given rpm, both phases have within .1 or .2 volts of each other. If I rev it up, it puts out plenty of power. I never revved the bike real high but somewhere around half throttle each side was putting out > 75vdc. After speaking in depth with the guys at Baja Designs (they've been probably as good about customer service as one could be without the bike actually in their hands btw) one of the techs mentioned that under no circumstances, should the bike be run in a single output (200W) without the headlight being on to absorb some of the juice or the R/R might be pushed past it's limit.... which is in the neighborhood of 160W. It's possible that I did just that in the beginning since at first I had it wired to use all the settings on my handlebar switch (Ign. Off>Ign. On>Low Beam>High Beam) and sometimes didn't bother to use the headlight. Who'd uh thunk? I hate things coming down to the wire and having to "crunch", but I'm going to Big Bend regardless. I would rather not be "riding dirty" with no lights though. I was even wanting to buy a set of pannier racks from Monkey Wrench ^^ but without knowing how many more parts I'm going to end up buying, that idea got "prioritized". Sorry Frank... I'll keep checking, and if you still got it when I get some 'rat killing' done, I'll get with you. 
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Tomorrow, I'm going to hook it up to the other lighting coil and make sure that one will operate it too, although I don't see why it wouldn't since it had the same output readings. Although stranger things have happened in 'electroland'. It's got to be that R/R.
