I think everyone beat me to it, i was going to suggest MachV and Andrewtech, they both have great reputations and a large following in the suby world. MachV is having a big open house, meet, carshow, charity event on the 18th if anyone wants to come up and meet the guys.
Andrewtech are considered gods in the nasioc community. They do specialize in trannys and gearboxes like Flat4 said but they do other things too, engine swaps, installs, etc. I just emailed them about installing my turboxs uppipe, since i dont have the time,experience or a shop to do it at. They quickly got back to me with a price that was considerably lower than any other that i had got. I will probably take it to them to make sure it is done right