Bell-housing alignment help
But.... but.... but..... Mammoth Motors TOLD you they factory would never have done that..... LOL. Golly, that is something. Good work to find this out.
It is a fair assumption to say that the trannie mount flange is parallel to the front flange of the bell housing. It probably IS parallel when the bell housing is torqued in place. But with this being so far off, I think it would be wise to torque the bell in place, and run the indicator around the trannie mount surface to be 100% sure. It is a smaller surface, so the amount of deviation from a flat plane will be considerably smaller than the block surface.
If you don't have the heads on but do have the pistons in, or ready to go in, then I'd first take the same piston/rod and mount it in holes 1, 7, 2, and then 8. Look at the piston-to-deck height relative to the location and see if there is a pattern of the deck piston-to-deck heights. I just wonder if the mains bore is off. Of course, it would have to be waay, waaaay, waaaaaay off for the back plane of the block to be that far off though, so it is not likely.
And there is another possibility.... that the side flanges of the back of the block have been tweaked backwards. But I'd think that the deviation would mostly be gone by the time you reached the areas of the block where the water jacket joins the rear flange, and that is not quite the case with your measurements.
If the bore is basically straight relative to the decks, then I would look at the shims like suggested. And I would consider putting the block to bell braces in place on this one.