Ah. I had seen a lot of references to assembly lube when rebuilding the engine, but only if I got deeper than the lower crankcase, so I was able to ignore all of that. Now I know that it'll destroy the main bearings if I do get that far (I know it was bad, but not how specifically bad).
At this point I am wondering if I have destroyed the bearings anyway, though, given the noise and the misalignment. The engine has been turned over (by starter and by hand) maybe 40 times since this problem appeared, but I imagine that with the forces involved, just once was enough to wreck everything. I have no idea where to get new main bearings (no luck on RockAuto), assuming that this hasn't also damaged the block itself. Which means I might be getting a new engine either way -- but I won't jump to conclusions until I see inside the engine.
And I do have the alignment dowels in.
Thanks!
-- Joe