Setting the gears and bearings on a differential is very time-consuming, but really not all that difficult. I've done it several times on Saab transmissions (FWD car).

The hardest part is getting the pinion projection set. That can be done with dye to check the gear engagement if you have a lot of time, as it will take assembly and disassembly of the whole unit several times. Otherwise, I suspect that there is a factory tool to check this dimension, as on the Saab.

You will probably end up buying shims if you go this route, as you will be unlikely to get all the shims you need for one mixed unit out of the two originals.