Tear it apart and start with all fresh stuff. If your on a budget it just the manhours to clean it all up but I would crack the oil pan to make sure it is still good. You can clean it up check the rods, piston skirts and maybe remove the head and clean it all up check for cracked valves or problems with the valve seats.
You can do a lot of work short of a rebuild and still have a good motor.
89YJ 2.5L TBI, AX-5, NP231 SYE, Tom Woods Shaft, 33" BFG T/As, 4" lift.
AF Jeep Club Tail #184