I just did a 98 ZJ swap into my 2000 XJ -- ZJ engine has 27,000 miles on it
Your 2000 had a 0331 head -- you need to address the difference between the 0331 head and whichever head you have on your 96 -- the exhaust, intake ports are different -- this adapter plate makes them all work together --
https://jeepexhaustadapter.com/0630-head/ -- worth every penny in my opinion
You'll also need 2 intake/exhaust gaskets -- the one for the 0331 and the one for whichever head you have
I used the coil rail for the 2000 temporarily -- just laid it on the spark plugs -- it sits there, a little tight with the oil dipstick tube -- Check out this thread for another option --http://www.naxja.org/forum/showthread.php?t=1066869
It's cheap, and I'll be doing this shortly -- already bought the coil from Rock auto -- Was under $40 IIRC
Cylinder #1 needs to be Top dead center on exhaust stroke -- finger over #1 spark plug hole -- air pushing out at you -- then you set your camshaft position sensor -- line up the holes using a toothpick, paperclip, drill bit -- search

for proper timing setup of a 2000/2001 -- it's really easy and not critical -- get it close and the PCM corrects
Any questions, ask -- Having just done this It's fresh in my mind