Ha. Yah, I would happily set fire to any part that is not working properly. At this point, I am willing to try any possible solution. That said, but for fueling issues, the ECU seems to control everything else correctly, so it seems unlikely that there is a hardware issue with the ECM and obviously the software has been changed multiple times. One of Toyota's FFV "fixes" was to swap the 3 speed fuel pump with an updated 2 speed pump. It seems like the issue might be the engine is not getting enough fuel to keep AFRs rich enough. Just like the how the Unichump was not able to properly compensate for the increased airflow, on my truck it seems that this this current tune/pressure switch/fuel pump switch is not able to increase fuel in a timely manner as needed.1-2 has never been a problem, its always been 2-3 which is what the unichip did as well, i have a theory from some information that i've gotten recently, but i do know that bullydog has a truck on the dyno to address the shifting.
If i were you i'd search around for a new ecu, trash the one you have, maybe light it on fire and shoot it in a box full of tannerite seriously do an ecu swap and i bet many of your alcohol % issues are gone. (the ffv ecu's are cheap on ebay btw & Jbroas can prob help you do an ecu handshake over the phone)
Maybe this A013 tune will provide some promise. Defimitely report back if you see any good results.
As far as the shifts, the issue was always 1-2 for me.