leo72:
You can use ArduinoISP to burn the firmware
That ended up being exactly what I did. The problem was that I had no Arduino board left with the serial bootloader installed, so I was catch-22. I had to do a Radio Shack run to pick up a new Uno -- luckily they close late 
Also, I now have an additional 1000 uF on the input to the LM350 regulator (the regulator needs to be beefy, because it also runs a servo -- hmm, that's also a motor ...) And a 6.8V 600W TVS across the input to the AVR board. I figure it can't hurt