At the very least - motor, all accessories, engine compartment wiring harness from a '96 and engine computer from a '96, motor mounts, etc. Radiator probably. You won't be able to use the '99 computer and harness without adapting them to work with all the emissions junk and stuff from a '99, and also the interior wiring harness and dash harness. Unless you've got both FSMs, some electrical expertise, and a lot of patience, it's not going to end well - you'll need a dash cluster and other stuff from the '99 also, it will really be easier to find a '96 6cyl engine harness/sensors/computer as '96 was the most-produced year for the XJ and the 6cyl engine was the most common.
You will also need the flywheel, possibly clutch and associated parts, and clutch housing (bellhousing) from a '96 or similar years with the 4.0 and AX-15.
So, to clarify, parts list:
* bellhousing and clutch, clutch housing spacer (the aluminum sheet that covers the open end of the bellhousing) from a '96 or similar years 4.0L/AX-15 equipped XJ
* '96 engine wiring harness, engine compartment wiring harness, sensors, etc etc
* '96 ECU from a 4.0L, either AX-15 or AW-4, will be easier with one from an AX-15 equipped donor though
* radiator for a '96 4.0L
* throttle body from a '96 4.0L?
* motor mounts and possibly brackets from 4.0L
I think the exhaust manifolds and such should just bolt up, and the 99 intake manifold will give you a few more HP supposedly, you'll need a '96 down throttle body for it *I believe* so that the '96 wiring harness will plug into the sensors, though you can probably splice wires without issue to make the '99 throttle body and sensors work.