since you have the 88 donor, its a simple R&R(remove and replace). you will also need to check that the pilot bearing will except the auto trans, which will be easy to inspect/replace when the manual trans is seperated from the engine.
you may want to swap axles also if your running larger then stock tires.
the xj with the manual trans came stock with 3.07 axle gearing while the auto trans xj will most likey be 3.55 gearing. 3.07 gearing with an auto trans will have poor bottom-end(power/torque) performance which will be noticeable if you run larger then stock tires, tow, have it fully loaded, or on steep inclines. only benifit would be that you could really whined the gears out and have a higer top end(speed/hp).
what is the reason for the swap? as mentioned, an ax-15(manual trans) from an 89 1/2 and up xj would be an easier swap.
