Grunt, a year or so back, I was wondering the same thing.
OK, quality on-line builders seem to get about $3000.00 for an R55...that wasn't going to happen. Same thing if you go to the parts house $$$$. Local shops will charge quite a bit too, $2200-3800, but as we all know a transmission R&R is no small thing, plus they have to warranty, so I can kind of understand their position.
On the other hand, you have your eBay builders, prices start at around $625.00 plus shipping, plus core or core return. 12 to 36 month warranty. Hmmm? $625? No freaking way they are doing much to those units for a measly $625. And, by their OWN accounting, as many as two thirds of the returned cores have nothing wrong with them!
If I KNEW my transmission was blown, a salvaged unit would have been fine. Because, on a high mileage SOHC, there was just no way I was putting 3 to 4 grand in the transmission. And the internet transmissions, well, I would have went that route if the shipping & logistics weren't so hectic (rural area, no loading dock here, so another fee to send out a lift-gate truck, etc. etc.) .
So, what I ended up doing, was just fixing it all myself (turned out to be a TCC System issue). You know, overhaul, valve body, upgrades, shift improver, and a re-man converter.
I know that is not much to go on, but that is just my own experience. Best wishes.