[gtmud]

Before you go to the extreme, check a couple things first. Cylinder compression, ignition system(are the cap,rotor,plugs, wires in good shape. Any fouling of plugs) try to adjust your carb's rich/lean jet screws to even out the rough idle. What oil presssure are you at? These are just some of the things to look at. If the compresion test is good then you might be ok, that is as long as your oilpressure is within specs.
Not sure whats involved in changing over to the 4.0, but I'm certian that most of the engine compartment items will need to be changed over. This resulting in having to buy a wrecked jeep and robbing all the parts from it. It can be done, but its no easy task.
Look at these few things first then go on from there.