I think I got it...if this is correct with what I am looking at for the E46ZST.000, particularly the E46 330Ci.
According to this:
These are the only three I get to pick from. BN51, BN52, and BN53. Mine is a BN53 from various VIN decoding plus going to realoem.com and entering in the VIN. So seeing how mine is a U.S. model, and the other two are Euro, my GM number will not change, unlike for the E36 recoding/reprogramming. So, as mentioned in Neil1138 (e46fanatics) link in a few posts above:
http://forum.e46fanatics.com/showthread.php?t=659314
He only seems to mention the SA code. I strongly believe now that this is correct with looking at the E36 instructions and how it examines the GM code in the NCSExpert data files.
I'll have to post my own E46 programming write-up when my time comes. There is also the coding bit about recoding the cluster (kombi) to have it disable the transmission gear display.
I used the SA decoder/encoder here to get my new SA code. If I am correct, all I needed to do was to uncheck "0205-AUTOMATIC TRANSMISSION" then re-encode it to get my new SA code.