I have installed the engine/tranny numerous ways..... I'm sure I'll catch some flack for this, but it seemed the easiest when the tranny was bolted to the engine and I put it in as a unit....
wish i could do this, but it'd probably take me more work to do that. because i'd have to first remove the engine and then install both the engine and tranny @ the same time..
You will find that the conveter will only bolt up to the flexplate one way, its always a good idea to figure that out and mark it while the tranny is out, I usually squirt some spray paint on it.
and i'm not 100% sure that i know what you're talking about on the torque converter only bolting up one way to the flexplate. how do u know what way it needs to bolt up?