Man, that sure looks nice!
Only thing I'd probably have done differently (maybe you did and I just don't see it) is put something between the bottom board and the lower part of the transmission case - like a piece of wood blocking. As it's shown it appears that the only thing holding the transmission from potentially "flopping around" inside the case is the shear strength of the four bolts (and plywood) at the end of the bell housing, and the shaft at the opposite end. Probably enough, but I've worked for UPS in the past and know how stuff can get treated. Honestly I'd have probably then put a plastic bag around the whole thing and shot the entire crate full of expanding foam too, just to lock everything in place. But that's just me. I'm paranoid like that.
That case is a beautiful piece of woodworking though - looks great!