I hooked up the battery to a powerful battery charger and jump starter at my friend's shop, and cranked at 13 Volts. Still wouldn't start.
I also went today and pulled a FJ Cruiser ECU from the scrap yard, and hooked it up to my truck, which gave the exact same result. It fires up without the UCON but not with it. I was surprised that it fired up without programming my key on it!
Anyone got a wiring harness diagram, to compare it with mine? Perhaps something is missing.
Also, my Fortuner is an Automatic, and the one I tested it in, which worked, was a manual. I wonder if that makes any difference.