The intended use for the truck may also affect the clearance required.

I find the factory clearance to be more than generous. The factory ride height is pretty high too.

I had an 87 D100 and did the same 8 1/4 rear to 8 3/4 swap. Like Kunkel said, factory numbers require a slight trim but I did not shorten mine and had plenty of yoke to seal clearance. Even at a lowered ride height plus towing and overloading the bed the yoke only went forward another 1/8".

If you have clearance but the balloon seal is touching. They also have rear transmission seals without the balloon.