Had a couple minutes to look at some more stuff. In this video I'm reading the raw cam signal (G2) coming in, and am reading the processed cam signal on JP2 pin 18 on the silver MS3 board. In a nutshell MS just takes the sine wave signal, and creates a square wave based on where the raw signal crosses the 0V line. Thanks again Shane for the scope, I wouldn't be able to do any of this if I didn't have it.
http://www.youtube.com/watch?v=t3eBiVhBgWo&hd=1