The tranny mount plate for the 1G bolts right up to the 2G tranny, perfectly as you describe. Even the speedo gear system which is electric on the 2G swaps right over. The flywheels are different, even between those flywheels that "Should work" I had a Findanza aluminum flywheel came right off my 1G tranny setup, would not fit into the 2G tranny at all. After replacing the flywheel with an ACT, the starter would not hit it very well. I had to bore the mount holes out a bit just to get the starter to contact the flywheel gear ring.
I vote 1. My bet, the flywheel is the wrong size for the tranny. 2G flywheel, 1G tranny. Here's what I'd do. If the motor spins by hand, and the starter is working, then the issue is clearly going to be in the bellhousing. Yank the tranny. Leave the clutch and flywheel on. Take the starter and line it up with the mount holes on the tranny mount plate and see if it is going to it the ring gear. You should be able to eye it, and I don't think the mount plate is strong enough to take the torque of the starter if you through bolt it onto the plate and try and kick over the ignition, but I've never tried so, ehh.
Just what I'm thinking, having dealt with similar.
/brox