Quoted from ChrisVW:There are two leads attached to the PWM 2/3 headers and those are the only IO's used on the board. I'll see if I can read the data somehow this weekend or explore other avenues.
The lamps on MG are controlled by a dedicated serial chain lamp controller (the arduino) feeding a strand of serial RGB LEDs. The two wires are used to feed data to that serial chain. The commands should be coming downstream from the PC via USB serial line. Those shows are controlled from the python game code running on the machine which is pretty much a hacked version of pyprocgame (open source) that was created because John didn't want to use someone else's control system and wanted all of his own crap.
Aside from those of us who bailed out on the project WAY early, there were pretty much two "programmers", one who made the hardware interface, and the one who did the game code (whom everyone knows, and who has come and gone).
If you want to change something with the light shows, you should be able to do it from the python code running on the game instead of having to sniff out packets.
EDIT: I also fully endorse hacking the POS codebase that MGs shipped with to make it a great game, and I'm willing to assist in any way that I can. Feel free to sue me, it'll be nice to talk to John again on the phone.