FYI, I got the car back on the road with the TRD AT ECU. I've gone through the wiring harness at the ECU and found a few wires that maybe "suspect". Hopefully this will allow me to get the Catback done and turn it over to a local "tuner" and get the Greddy EMU in. I hope the TRD ECU pinout helps some people down the line.
05 Matrix XR 4WD and 03 Vibe GT
"If you want Government to solve your problems, then you are the problem!" BMSR
Trix MODS: SRI w/ AEM filter, Vibrant/Magnaflow Cat-back, Alutec Lightweight Crank Pulley
GT MODS: Cosmo SRI, DRL, Auto Stop