A friend of mine just recommended a shop who has quoted $1300 to rebuild the transmission. Supposedly they normally charge $1700 and that is with a discount. I am not sure if "rebuilding" implies a standard procedure but I am guessing $1300 will just fix what's wrong vs. replacing all wearable parts. Not sure what else is done above and beyond by a dealer or a place like TEP on their rebuilt transmissions. If I go the TEP route, I am looking closer to $3000 - $3500 assuming I find a shop willing to just replace a trans if one is shipped to them.
On a side note, I would like to take on a project like this myself but it is winter time and I no longer have a garage to do repairs or the time to do them.