Well, crap. It didn't start after I returned home from church today. It's getting zero crank or cam signal when I attempt to log it. However, if I jumper power to the crank sensor and look at the signal with my oscilloscope it puts out ~10v square wave. That was with the MS unhooked and a pin in the connector to back probe it with the ground hooked up to the sensor signal ground.
I'm at a loss on this one. I'll be calling DIY autotune tomorrow to see if they have any suggestions. I'm wondering if feeding the hall sensors off of the 5v reference signal didn't damage the unit somehow?