Well, I figured out why the cam signal was off. After some emails back and forth between Henry at AEM tech support we decided the problem was the cam sync. So he asked me to take pictures of the inside and send them to him so he could be sure the cam sync really does trigger once for every one crankshaft rotation like I was telling him it does. I took the cover off the MSD cam sync and found a surprise waiting for me. Take a look at the photos below:

The stuff that looks like fuzz is really lots of tiny little pieces of broken magnet. This was the reason why I was getting strange input from the cam signal. I also noticed the magnet inside the shaft was loose and moving back and forth, which I can only guess is the reason for the pieces of broken magnet everywhere. No wonder I was having problems! I spoke with a tech at MSD who told me even though it was out of warranty to return it back for a free fix. Im not sure how long its going to take to repair and send back, but this really puts the pressure on for getting the car ready by Fun Ford Weekend in March.