Michael, start with a commpression test, that will tell you the valves, piston rings, and cam timing are correct. If you have good compression 100 lbs plus then take the valve cover off and turn have someone turn the engine over while you watch each rocker arm. If they all move the same amount then the cam lobes are ok and the engine is probably ok.
With the timing, if your off even one tooth on the distributor it will cause the symtoms you mention. Try moving the dist one tooth ahead and back and see what happens.
Also sounds like it could be a crank sensor problem too as this is common on Jeeps.
Keep us informed.
Kel