Try an non-subaru shop. I had my trans replaced last fall with a rebuilt tranny for 1,725 at a tranny shop not connected with subaru. I called every shop in town and asked if they had ever work on an SVX and for a quote. The shop that had done the most SVX's said they didnt do have the stuff the others said they had to do to fix it, so the cost was way lower than the other shops and it was way less labor hours than he quoted me.
I love my tranny guy.
One scary side note about my tranny shop, the ONLY car they have ever had broken into was an SVX and its entire dash was stolen. It was left over night by the costumer in the side lot (something they say not to do. They only park it there for pick up) He was great with my car, he put it in the bay the right after they test drove it and left it there until i picked it up. I really really love my tranny guy.
I'd like to have done the 5 speed swap but my car is getting up there in age, mileage, and has enough problems to make it not really worth it. (not to mention i cant drive a stick!)