Referring to this thread:

https://www.miataturbo.net/forum/showthread.php?t=20474

Not Bruce's fault at all, but a head's up to anybody running the EMB with the Autotune. Turns out I had a combination of a loose O2 senor connection on the pressure switch and a short accross two of the poles.

I had secured my pressure switch underneath my glove compartment, but at some point it came loose. I think my GF might have stepped on it a couple of times getting into and out of my car, first loosening the O2 connection causing the initial problem. I finally figured out what was going on when two of the poles on the pressure switch were eventually bent together enough to cause the short, keeping the red light on the Autotune on long enough for me to notice.