Not that I'm an engine expert or anything, but from everything I've read, apparently Ford and Chrysler swaps are the hardest to complete into a TJ. The 318 shouldn"t be any exception to this, and apparently the 904 may be the only transmission (auto) that fits up to the 318. Plus, considering the 2.5L, you're also looking at some adapters or new drilled motor mounts. This project is a HUGE undertaking, and I personally would rather go with the Vortec V6 or a Chevy Gen III engine (LS3
) then mess around with the wonky 318. I've also heard the AMC v8s drop right in (though I don't know with the 2.5L) with fewer modifications necessary.
Also, keep in mind, in many states if you change out your engine, the engine has to be from the same year or newer then the car or you fail emissions - the only thing NJ now checks for