Block out of square

Others may not agree, but if it was mine, I'd machine the bellhousing to correct the problem. This would allow the centerline of the crank and the trans input shaft to be perfectly in line and true. Yes, the bellhousing and the motor would be paired for life, but that would be a better compromise than trying to disassemble, correct or return the crate motor. I would have to assume any significant engine disassembly would void any warranty as well... The fix is in the bellhousing.