well the ford 8.8 is a rear axle, its a hair shorter than stock but not a big deal. its a good swap. the best dana 44 rear for a yj is out of late 80's xj cherokee. harder to find, only available for a couple years, if you find a comanche rear d44 thats fine to. these axles have the same bolt patterns as stock and very similar lengths. the 8.8 is very abundant, and found in explorers, disc brake axles were from around 94 or so on.
the front is gonna be a different story.