Block out of square

There are numerous problems with this situation:

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As you can see from the pic I drew, if you mount the trans the way things are right now it will cause the trans center line to be misaligned with the engine center line. This is only true "if" the back of the block is actually "not square" with the crank. The other problem is that if the threaded holes in the back of the block are "square" to the surface (which they should be) they will also be out of square when you thread in the trans mounting bolts (after you machine the block back face square). If the bolt holes are square to the engine block surface and you machine the surface square to the crank center line the threaded holes will no longer be square to the surface. It's really a complicated problem until you find out where the actual problem lies. If the bolt holes are currently square to the block face and you machine the block square, then mount the trans, the underside of the bolt heads (the ones that go against the back side of the trans flange) will be cocked because the trans flange surfaces are parallel but the engine bolt holes are square to a different surface (the old original out of square surface). No simple solution until you find out where the real problem actually is????
Sorry about the poor drawing.....Treblig