Axianator
I am a banana!
Yikes! I certainly don't envy all the issues you've had with your transmission...see thread for transmission not working information. I doni't think it is tune related.
http://www.shoforum.com/showthread.php?p=800694#post800694
If you're using factory values for your transmission functions on a rebuilt unit, then I would agree that the factory programming would not have much (if anything) to do with your current situation. More than anything, it sounds like an internal mechanical issue that popped up as a result of your parts reassembly process, which may have been aggravated by the final drive change.
Speaking of which, I notice that you haven't mentioned whether your gear ratio scalar changes were successful...
If you've been running calibrations with an Engine Torque table whose cells all contain a value of 300, and you've been doing this for the past several months, then you have almost certainly caused internal damage to your tranny.I viewed my onld tunes and it seems as though i've been running with the torque table at 300 across the bord for a long time. that kind of sucks to hear.

Unfortunately, I do not have a transfer function on-file for that particuar MAF.Not to high jack the thread at all. Just wondering where I could get the MAF calibration codes and files (or whatever I need to program it)for the FMS 76mm MAF.
Unless someone here has a calibration flow sheet for this MAF, I would recommend that you pop over to the Yahoo! TwEECer mailing list and post a message requesting the transfer function values for this particular MAF. If you're lucky, someone will provide you with an approximate 30-point transfer function for that MAF that you can plug directly into CalEdit.