The Internet just ate my post. Let me retype it...
Last year, 177 had a system where we had a wireless serial link using SMiRF radios and
Kevin Watson's serial code. This let us interact with the robot and send it commands to change various PWMs or anything else on the robot on the fly. We just had some code that looked at what we were sending it via serial and changed things correspondingly.
Basically, you want to do the same thing, only wired instead of wirelessly. I would recommend looking at Kevin Watson's serial code as a starting point.