I'd jump into the performance/engine section, which has sub-forums for the transmissions. Should be able to find some good info in there. In the meantime, I don't see any reason why the bellhousing would be different between auto/manual, but that might be a decision the guys at the salvage yard make for you. On the plus side, a transmission shouldn't cost much more than $200 or so, imo.
I had the flexplate-to-clutch bolts fail once at about 8000rpm. Turned the clutch and flexplate into sawblades, pretty much. Cut a nice hole into the transmission. Cast aluminum can be a bitch to weld, but it's possible. Should you end up rebuilding the transmission at all, you might consider picking up some safing braces for the diff and a new input shaft bearing. (Or was it output shaft? Meh. It's been four years or so...)
