Suppose this thread deserves an update.
My tuner had a 6 hour come-to-jesus chat at SEMA with the guys at ECUTek regarding firmware mismatches and incompatibility with their software and ECUs - in particular mine. After some forced hands ECUTek agreed to bench my ECU, repair it, and load the proper firmware to match the ECU's version.
Sad part - they are based in Europe.

So my car is down at Drift Office without an ECU for the next few weeks. While it is just sitting around they are going to do a complete inspection of my turbo kit to make sure everything is all good there.
I have heard that a Motec M1 will be showing up at the shop soon and might end up in my car to see if it runs fine with that installed rather than the stock ECU... If it does I don't know what I'll do. Really don't have $3500 kicking around to buy another Standalone EMS...
So for now I am back to Daily Driving the MR2. I'll take some pictures of it this week of my winterizing process, as my MR2 thread deserves a bump.