Sharp, IIRC the XJ/MJ 2.5L water pumps spin opposite the TJ/YJ engines, is that what you're thinking of?
You can use the '97 throttle body if you change any sensors that have plugs differing from your '93, and cap the vacuum port to the MAP mounted to the base of the TB.
You will want to reuse the YJ fueling system, it's the largest difference between those two motors.