Most likely something silly like a wrong connection, a pinched wire or a loose connector. I can only give some suggestions of what too look into.
Aside from the T-harness there is can-hi and can-lo (which i would think is fine since the unit programmed) and then there is the driver door pin and the parking lights you would want to look at.
That driver door pin is purple/green. Ford likes to put purple/green (or purple/something) on 80% of their circuits. Right now, my money is on this connection being on the wrong wire. Ideally this should all be tested with a meter or logic probe.
Not sure how you tested it, but when removing the evo, also remove the t-harness and put back the factory harness in it's place.
I would just call us though as it might be simpler to help you out this way; we're open from 8am EST. 1-877-336-7797. Have a testing tool ready. And just to be sure you had the proper installation guide, I'll assume you installed this for the 3xlock start feature, make sure you followed the programming of the unit written in this guide: Stand Alone Installation with T-harness for Automatic Transmission only
Unit would program but wouldn't remoted start. Blue light flashes when lock button is depressed.
This is due to something else. I don't currently see any options enabled via the service number you gave. If using the 3xlock start feature, options C1 and D1 need to be enabled in the unit. Need to get the vehicle back up and running normally before dealing with this though.