You absolutely owe it to yourself to get ahold of Bill Kondolay at DTT, hopefully before the shop gets too far into the repairs. He will give you a world of advice, the best TC and/or valve body available, or in your case, maybe a completely rebuilt transmission for close to the same price.
The stock trannys are junk (as you may know by now). Putting another in now, will end up costing another rebuild later on. For the extra money, this should be the time to get one that is built to last.
I dread the day mine goes (and know that it will), but look forward to getting one that will perform as well as the engine.
I don't have his 800- number, but could you can find it on his website (see: transmission shops in the "links" page).