BroHogan, those are prefect. Thank you!
MikMo, I'm probably going to put the Atmega168 chip right on the board. The BBB and RBBB are possibilities, but I think that if I can handle soldering chips to the board that I could be able to also provide the most minimal configuration to support the AVR, and put it in a DIP socket so that I can reprogram it via the Arduino board if needed.
I don't think there's a way to tap into power from the camera, and I don't really want to do that, anyway. I haven't investigated to see what's available via the remote port wires I'm hacking into, but that doesn't seem like a very good idea (especially if I ever want anyone else to use it with their $1,000 camera...). I've also attempted to make it "sleep friendly", in that it will wake the camera if the camera is set to go to sleep after a certain period of time. I recently bought a small truckload of AA and AAA NiMH batteries for my PocketWizards and flash and want to try to re-use those. It looks like the step-up converters that BroHogan pointed me to could potentially operate off a single cell (but more likely at least two). Hrm, I wonder what kind of runtime I can get out of a lithium watch battery?
I do want to minimize the footprint of the enclosure as much as possible. My component list is very short: two 6-pin DIP optoisolators, maybe 10 resistors, and then the Arduino, of course. I should be able to pack that tightly under the LCD board. I'll probably start at Radio Shack to find the protoboards and boxes. I was disappointed to see how poor Jameco's site is at finding a suitable box, but I haven't gone beyond there yet.