what kind of engine u want stuffed in there? if ur debating an old chev 350 its not worth it. for the additional 40HP might as well stroke out the 4.0l in there. (get it built) that'll net u more power than a bone stock 302 or 350... if u have a 4cyl, umm............. stroke a 4L and throw it in there.
if u wanna do a crate motor ur looking at new transmissions too, and to pay a shop to do it........... good luck, completely custom jobs will always be costly, and rarely come out the way u want it. if u want a HEMI or something along those lines, (aka crate motor) ur looking at 10k easily once its all said and done. you can get some quotes for less i would bet for sure, but after its all said and done, your engine swap will be worth 5x the jeep.... and you still need axles unless ur runnin stock tires
i'd pay to have 4L stroked and toss it in the jeep.