I most certainly agree that a swap involving engines and transmissions that were not originally designed will no doubt be very involved just to get them mounted correctly and work right as well . Which will always involve adapters that are costly. Hence the phrase "labor of love".
carburetors will always command our attention . You can do the best rebuild , sealing fuel bowl leaks , float setting , choke setting , etc. , and eventually will have to be done again . Floats get gas logged over time necessitating rebuild , gasoline just has its way of doing its deeds to internal parts , especially the new ethanol gas . Fuel injectors need attention too but no way near what a carburetor does. Some carbs are just troublesome by design. I like carbs because I used to take pride in rebuilding them but F/I has many advantages , especially for off roaders . No more float bowl slosh and bog on hill climbs. As far as V8 swaps , if you really want a V8 , I could understand , but for practicality and simplicity to spend less time tuning and maintaining , it is best to seek more HP/TQ from your existing engine or upgrade to an engine in the same family to keep installation simple and inexpensive. Not even just jeeps , I once had a hand in putting a small block Chevy in an AMC rambler which NOTHING fit and we had to engineer everything.
Adapters are available for so many engine/trans swaps but it all comes down to $$ .
i would definately go with the 4.0 swap as it replaces a 258 and will work out much easier . Just make certain that all your parts match so that it will be a true bolt in and nothing left out such as trying to get a CPS to work with a bell housing that never had one , for example. I think a 4.0 will be all you need and is not an over complicated swap as CJ's and YJ's had I6's so will just come down to wiring for PCM and a new fuel system.