I'm still intending to put a scope up to the communication pins on the black box microcontroller at some point, but I don't expect to see anything, or if I do, be able to have any sort of effect on the system.
So the clear solution is to pull the microcontroller off, and then solder some headers in its place. Like how SMD JTAG headers are done.
With a daughterboard that connects to those headers, the world is my oyster in regards to hacking projects. The most obvious first step is to add a Hall Effect sensor, so I can detect wheel rotation.
Other than that, I was able to almost wholesale copy the schematic from #PIC-On-The-Go, which means I also have all of the components on hand. It really was the perfect pinout. I have enough space to do everything I want, and nothing more.