Ok - I was thinking there was no kickdown, but your problem is upshifting. Check to make sure you connected the line pressure cable to both the tranny and the throttle body linkage. If you had a problem with the ECT ECU before the upgrade, it might just be that ecu - try swapping with someone...
the avc-r is notoriously bad for displaying speed. You will throw a code if your speed sensor is bad. Are you throwing any codes? Will it kick down from o/d to 3 at wot? Here is the troubleshooting guide:
http://www.cygnusx1.net/supra/library/TSRM/at/AT_011.html
put a train whistle on your drainpipe there and be the next bubrubb
wooootttttt-wooooooootttttt
Or just run an inverse divorced downpipe - run the wastegate to the exhaust, and dump the rest at the elbow. That should run like 4 seconds faster in the 1/4 and smog just like stock.
A 4 or 2 gauge high quality wire from the alternator bracket to the body helps. Also make sure your battery posts aren't corroded. I never saw much more than that with the stock alternator though. I'm running a 150 amp unit now.
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