If you pop off the rear diff cover, you should see the gears. Put the rear of the jeep on jackstands with the wheels off the ground (trans in neutral) and spin the wheels slowly looking for chipped or broken teeth on the ring gear.
If its chipped, take out the carrier, clean all the metal shavings out, and get a new ring and pinion set. (Count the teeth on both to make sure you get the right ratio)
If its not chipped, it could be elsewhere in the jeep, or elsewhere in the axle, you could pull the shafts and check them for wear but i doubt it would be them.
The ford 8.8 swap is a common thing for jeeps because its ~30% stronger than a dana 44 with its thicker tubes and larger diameter shafts.