ok, you gotta couple important things to consider here:
first off, you gotta find out the smog/emissions laws in your state regarding your jeep and diesel. in Georgia, metro counties are required to pass certain emission standards, but diesels are exempt.
in the case of an engine swap, the BODY of the vehicle is what the emission folks go by. so in your case (if you were in GA) your MJ would still be required to pass. on the other hand, if you take a volvo turbo diesel and swap in a small block chevy, it is not required to pass because the body is registered as diesel. so you really need to figure out how you will get around the smog situation.
the liberty transfer cases should be the NP242 and the NP231, which are labeled selec-trac and command-trac. both are very similar to the units used in XJs. the 242 is not inferior to the np231, but it does have less aftermarket support. the np242 is an awesome transfer case, my brother runs one in his XJ.
let us know what you find out.
-Nick