Progress is slow on this machine, as we've got it up on a lift in my FIL's barn and I don't trust myself to be able to properly hold it all together while getting the bolts all in with that 4r55e hanging out around my head and shoulders.
As such, I haven't gotten the bottom bolts to fit in yet. However, it looks like the trans and engine aren't properly lined up. We're supporting the transmission with a board between the frame rails (where the crossmember goes, but it's out while we get everything together), and I'm thinking that the board is holding the back end too high up.
I've positioned a few tall jacks under everything (one under the tranny just in case, and one under the engine), and I can tell that everything lines up better once I push the engine up a little (but then the supporting board comes out, so it's a scary game).
I've got a busy weekend, so I can't touch it until at least Sunday. My next plan will be to jack that engine up a hair and, with a few volunteers to support the transmission, undo the top bolt we got in it just enough so that the bottom can come back into alignment. I suspect/hope that those bottom bolts will fit into the threads once that happens.
I'll update this once I get it figured out, then maybe start a separate thread for the process of getting it all back together (plus additional work I need to do to it).