Block out of square

"Okay, but... How big of a deal is that, really? I mean, if I have a taper in the back of the block that's 40 thou over roughly a foot, then over the .56" width of the head, I'm looking at 1.6 thou of variation from one side of the bolt to the other? Seems like I can just ignore that amount of error. I mean, do I trust my washer underneath the head of the bolt to be flat to less than 2 thou? Do I trust the cast bottom surface of the head of the bolt to be flat to less than 2 thou of tolerance? Do I trust the paint on the bell on both sides of the hole to be consistent to less than 2 thou of tolerance? Maybe I'm thinking about this the wrong way, but it seems like maybe that particular problem is ingnorable?"

"How big of a deal is that?" Not a big deal at all if none of the bolt heads break off over time/stress. You could give it a shot and hope for the best. The only real suggestion I have is to remove the crank (leave the pistons in the bores), set the engine block upright on it's back face on a dead flat surface. Then use a good long machinist square to lay against the flat surface to see if the engine main bores are square to the back face of the block. If they are not you won't have much choice but to confront the people who bored the mains. Otherwise, "run what you brung"!!
Just remember that the trans input shaft is a snug fit into the crank pilot bushing. So once you stab the input shaft you're going to tighten the trans flange bolts which will raise the tail end of the trans about .050-.060" (if you don't have the back of the block square to the crank) and put undue stress on the end of the input shaft which will transfer into the input shaft bearing, etc, etc.... that would definitely not be a good thing???
The mind of a machinist is relentless!!! treblig