Saunders Transmission in Argyle, NY, it's probably 40-50 miles from Rutland. They have been in business over 30 years and if a local dealership is having trouble they usually send it there.
I had them do my clutch because I didn't want to do it in the driveway, they actually took the time to re-shim for the new input shaft to make sure it was correct and not just slap it together. They have a gas engine pulling truck with an auto that kicks butt. Their shop is nice and clean and it is a family operation.
I don't know what they know about highly modified transmissions but I'll bet good money they can help you out. Give them a call, it can't hurt.
Saunders Transmission Svc Llc
1022 State Route 197
Argyle, NY 12809
Phone : (518) 638-8838