I'll respond.... though I don't see how this really relates to my problem...
But anyway, I had a similar issue with having to have the computer reprogrammed. It cost me $50 and was pointless. The following day, all the electronic issues came back. Upon my own investigation, it turned out that the OBC in my car wasn't meant for my car. It came from a convertible 3 series which explained a lot of the issues I was having.
I don't know about reprogramming the transmission. If you need a new alternator anyway, go with it and see what happens. Though, replacing the alternator could be cheaper if you buy the part from the dealer and install it at a local shop.