I can't believe I ended up working on this thing all day again. Got the board soldered into the Les Paul. I updated the firmware to relay the button presses, but only 3 of them work so far: green, blue and orange. Yellow and red cause my test program to crash, I think its because there is a conflict in the firmware over that pin. Its the same pin that seems to be mapped to determining whether or not the chip is self powered and to detect the USB bus. I don't know why the strummer and all the other buttons don't work though. I think I have an idea of how to fix it. I'll have to look into that tomorrow though, I'm ridiculously tired because of the jump forward for DST (and staying up entirely too late last night).
So yes, that means the first firmware will be the "mod chip" solder in kind. And yes, it should still allow you to use the guitar for GH3 or Rock Band. For Rock Band, the guitar will be wired though.