Whoever said Diesel Transmissions were a religion was right!
Seriously, call both companies and go with the people you are most comfortable with. For me that was Clint Cannon and his family at ATS. Their knowledge, commitment to service and just the spirit of the guys who work there was really something! I'd go with them again in a heartbeat.
Also, if you have an ATS TC, it would be best to go with an ATS Valve Body. Without it you probably won't be able to shift locked, and what if you have a problem? Which company is going to warranty the trans? If the other make of Valve Body screws something up in the trans, and I were Clint, I wouldn't warranty it.