Yes! Well, at least somebody got it.
Along those lines, the Arc Reactor has always bothered me...it's just too convenient. (Yeah, yeah, I know...)
So, I got the charging circuit better assembled now...and ran into a few problems. First off, I accidentally blew out an I/O pin on my uC before I thought to use a diode instead of just hooking it straight in.... ..yeah, that's fixed now...feel free to ridicule. The second thing I ran into was rather unexpected...
Once I had a good switching rate (105Hz atm), I realized that the charge rate is waaaaaay faster than I was expecting from previous tests (100V in 1.9s!), so I needed to start playing with higher voltages to continue testing the circuit. So, I pulled out one of my 3uF 450V caps and let it run. ...now, the thing is, I neglected to check the limits of the transistor I was using before I did that, so I was rather perplexed when it stopped charging at 100V. ...and then ceased to work at all.. I checked the datasheet again, and it's actually 60V, not 100. So no wonder it burned out.
So, into the parts bin to find a higher rated transistor! Hurray for plasma TV parts!
Here's a shot of the circuit as it is now. Yes, I am being semi-safe and using fairly hefty jumpers and a 0.01Ohm 10W resistor to drain the caps when I'm done with them. Another benefit of the tiny capacitance of the cap I'm using is that it drains really fast by itself, so even when I had it up to 100V, by the time I had shut off the power and reached over for the jumper, it was down to ~35V.