MATT - Son's built probably a DOZEN or more 8.8 Ford rearends, one used behind a 500 HP small block in a Fox Mustang, plus worked for a local industrial gear box mfg. as an assembler for 1-1/2 yrs. The boxes he built were the size of a CC or larger, and weighed anywhere from 2000 to 5000 pounds. And he built thousands of them.
The pinions and ring gears are actually really close tolerance, the variation is in the housings, if you keep the shim thickness the same with the housing when you swap pinion & ring gear you are probably VERY very close to a correct setup for pinion depth, back lash, tooth contact pattern, etc.
It was actually FUN to watch him build his 8.8" for his Lightning last winter. The only parts we reused was the housing itself, and the axles. New ring & pinion, diff, all bearings & seals, crush sleeve and other small parts. He went from a 4.10 Traction-Loc to 3.55 Detroit Locker diff, Summit diff cover with pre-load bolts for the diff. caps. Took him about 35-40 minutes to completely assemble with Me handing him tools & beer! It's been the quietest most trouble-free rearend he's had in the truck in the last ten yrs & 130,000+ miles. We've got all the mic's, dial indicators, etc to check everything and when it was done all the spec's were to the tight end of the tolerance range, just where we wanted them.