I'm trying to find Toyota OE VVTi literature to confirm if there is some kind of special start-up position for the VVTi cam. With VVTi cam control, the start-up has been a little harder, not sure if its the VVTi mapping, or simply I now need to tweak start-up calibrations to work with the new VVTi cam position (over what OE was doing during cranking), I need to work on my hot start for sure. And got to test a low battery start-up, wow. Very impressed with the hardware and the contributor's code, was very surprised the car turned-over and ran with such weak cranking.
Gross Poluter, I'll be in your neck of the woods for about two months, would be cool to meet up, and if you want you can analyze my OE ECU's VVTi settings if you like, could possibly answer some of your pondering as to how the OEs tune it and why (though I think it would be confusing at times as they were tuning for different goals at different loads) . Can't wait to see what you find with the knock module. Oh, and is your setup prone to backfiring? I have a few backfires when I let off (hard to hear, I have two metal cats, resonator and muffler) and a buddy of mine (another 2jz VVTi) was having a lot of backfiring when letting off of the throttle (strait through exhaust, what a show).