You will need to weld on coil perches, control arm mounts, trac bar mounts, sway bar links, etc. The esaist way to do this is to buy a premade bracket kit and weld it onto the diff. This is the biggest obstacle.
ABS will probably not work anymore.
The axle is a bit narrower so you may need to add wheel spacers.
If the axle ratio isn't the same you will need to re-gear one of the diffs to match the other.
The 8.8 is a good upgrade for a mild trail rig and no matter what diff you upgrade to the above will apply.
Personally I'm not sure that the cost of upgrading an 8.8 to fit into a ZJ would be money well spent. A D35 could be upgraded to be as strong as an 8.8 for comparable money for what it would cost to put the brackets on an 8.8 and be a bit easier to do, no welding, bolt on sort of things.
What are your plans? How big a lift/tire, etc?