Almost everything will swap over fairly easily. Most body parts won't be an issue, except maybe hatch door/tail lights. Front clip is different style but I believe it would bolt-on. Doors should be straight bolt-on.
As for drivetrain, 2000 used distributor-less engines, that could be a pain to swap in to a 96 XJ. Also the automatic transmissions changed around '98 from a single-pulse per rev to 4-pulse per revolution. The tranny itself can be swapped over, you'd just need to keep the tailcone from your 96 auto and put that on the newer tranny, otherwise the thing will shift straight from 1st gear all the way through the gears into overdrive as soon as you get going over 10km/h.
Could you be a little more specific with exactly what you're wanting to swap over to your 96?