Well, the saga of El Rojo Grande (90 745ti w/m46OD) enters a new stage, DRIVEABLITY! My transmission transplant was a success, all the f**cking around after the transplant was completly unrelated to my efforts (at least it seems so). The mechanic I took it to found several reasons that the car did not work right, including:
1. bad (factory original) fuel pump (25psi instead of 80psi)
2. a bad knock sensor (I think that one was the real culprit, car was acting like the timing was not advancing properly)
3. bad fuel pump relay
4. dirty connectors to computer, resulting in bad signal interpretations form air mass meter (Thank God it wasn't the computer itself, $900!)

Lessons learned:
Be careful, trust yourself (if you deserve it), and find a good mechanic for those problems that just can't be solved by one guy who owns and works on one car (me). Sometimes the problem that appears after you fixed part A has NOTHING to do with part A.

Thanks to all who made sugestions along the way, some were pretty damn close, but it really took a guy with a meter and the Bosch School training behind it.