How difficult and what would i need to do a swap in my YJ to go from a 2.5L to a 4L or 4.2L? also opinions on all 3 engines?
Swapping in a 4.2 ? , pfffff , hardly worth it .
The 4.0  makes more sense , it's a bit of work though .  A rough list of  required items would include an engine / tranmission / transfercase package , driveshafts to suit your configuration ,  the wiring , exhaust system , the frame will need work , specifically the engine mounts moved.
Why not do a gearing change  instead , does the 2.5 you have now still run good ?