I went on vacation this past week so I wasn't left with much time to research or post. But now that I'm back, I have nearly finished my PCB for the ADC break out board, and I've found my answer to how the IR sensor works when it is mounted at an angle. My holy grail came from here, and I was finally directed there by Chebuzz over on the Paparazzi forums. My equations are:
Pitch=(x+y)/2
Roll=(-x+y)/2
Woohoo! Now to work on the GPS and magnetometer guidance. That's gonna be interesting! Ublox here I come.