Block out of square
From there, my observation is that the bell itself has a scalloped shape compared to the block. Thus, there's only actual contact in the area around the mounting bolts. Between the bolts, the bell doesn't touch the flange at all. So my next thought it to get a set of precision shim washers, in a range of thicknesses, such that as a set, they make the amount of ramp I need to bring the mounting surface back to true. At that point, I believe my dial indication comes out at or near 0, the angular misalign is corrected, and I should be good to proceed.
If your bell housing indeed does not contact the block except at the holes, then I can't see any reason to not use hardened shims/washers. You might want something to seal it up to keep dirt out.
Is this a non-stock bell housing? Sounds like it if you talked to the bell mfr.
I understand the concern on the pistons being at different heights. No way to know without somehow verifying. If the crate mfr did not catch the initial problem in the crank line, then I sure would not count on them to make sure things were decked in a way to make it even. You mention a dyno test? WHOSE dyno? The crate mfr? If so, how good is that?
At this point, I'd check couple of combustion volumes. Maybe turn the engine on the stand so that the plug holes are straight up on one side set the front cylinder precisely at TDC on overlap, and use a burrette with an appropriate oil to measure the combustion volume. The check at the back cylinder on the same in the same fashion. If the crank was inclined as much as you think, you are going to see a lot of CC's difference, like 5 to 10 cc's depending the head chambers, piston tops, etc.
Or just pull the heads. It sounds like you have had this engine for a while.
The crate mfr's reactions reminds me of a decking problem here a couple of years ago. The local shop jobbed it to a small machinist, who decked the block with an uneven slope on each side. Went to discuss it and the attitude was crap.... refused to look at my measurements at first, and almost ended up as a fist-fight LOL. After about 40 minutes, he slipped up while showing how he had lined something up.... voila, there was the problem. He saw it as soon as it did.....
The crate mfr doesn't know how good or bad any customer is at measuring and knowing what is what, and probably have plenty of cases where things ARE right in the engine. So you may have to stick by your guns with the crate mfr if you want them to fix it.
