If you want to keep it Jeep.... 304, 360, 401.
The GM 5.3 is popular and painless wiring offers stand alone harnesses (sp?) to simplify the instalation. GM uses common bell housings which opens up all kinds of options
I don't like Fords so .....
I have seen a TJ with a dodge 360 (different from the AMC). You could go with a 318 also.... all good engines and readily available.
Clear as mud, I know. My .02.....R