CB - I think the main thing you want to do is find a reputable transmission builder in your vicinity - someone you can trust. A good builder has a rep to protect and will steer you straight. Call SunCoast, ATS, Goerend, DTT and just talk to them - you'll learn a lot - after that your decision will become easier.
I liked SunCoast and got loads of good information from them (I really liked SunCoast), but their local builder/installer didn't return my phone call, so they were out. ATS - well... after reading a bit about them on this site I felt like they probably have a well-marketed product, but their local presence left something to be desired. I talked to Dave for a while and would have probably gone with him if he was somehow closer to my location. I finally went with DTT - I bought in to their philosophy of keeping MY transmission and just putting big, tough, proven parts in it. I didn't go with a super-trick multi-disc TC, just their single-plate workhorse TC. I talked with their local builder many times before I forked over the bucks (and lots of them... ) I was convinced that my builder was a bona fide pro from stem to stern - even visited his shop before handing him a check.
I now have about 25,000 miles on my DTT 48RE and it still yanks my fiver around with authority. I'm sure that most of the top four trans builders will do you right. I picked DTT and haven't had a minute of trouble - I'd do DTT again without a thought.
Make the calls and go with your gut. Good luck.