Hey, i just got finished doing this to my 98 zj last week.
I had a 92 xj that i was tired of F*ng with.
The most difficult was the pedals, but even that was not hard.
I took the xj pedals (brake/clutch) and zj pedal (brake) and basically laid them next to each other to get measurements. cut wedges out of xj pedall and hamered the top flat then welded it back together, i also cut a squar out of a portion and welded that back for integrity. (forgot why) using the xj cluster that "knock out" you can see in the zj firewall doesn't line up. you have to go further towards the center about 1-1.5 in.
things to come out: auto linkage, trans cooler lines.
have to cut a hole drictely under where the shifter was (maybe slightly forwad, but not much.
As i said i only got it finnished (driving last week, so still some kinks.)
the tranny mount was a bit tricky i used the xj one, made a spacer by cutting apart the xj cross bar (I don't believe this would swap i looked at it, but never tried ) and then also moved it forward a little by cutting a hole on the replacable portion in front of factory ones. without spacing it up a little the front driveshaft was hitting cross bar.
I found there is many CPS that were used. not sure how your's will turn out, but i used one from an automatic xj that was 98 as well. the auto xjs mount the same as the manual ones as opposed to the zj, mounts with only one bolt and too short, so you may be able to use the cps from the manual or possible use the year of your zj but from auto/manual xj.
The manual trans is shorter, most i read said ~ 3 added to rear driveshaft and - 3 from front. mine is lifted 4.5 so i had to actually add 5 to rear and only take off about ~1 from front.
my XJ/ZJ driveshafts were nearlly identical
NSS can be grounded to get engine to crank, or hook up to a switch on clutch, i think one of these wires turns on reverse lights (haven't fiddled with that yet.)
reminds me, i used the zjs brake switch which needed a square hole and my xj pedals had a round one, just took some "precise" dremmeling/hogging to get the zj factory one in rather than re-wiring the xj one.
don't know how it will work for you. i was crossing obd1 obd2..
I do have check engine lights, haven't even scanned them to be honest, driven truck about 200 miles since. seems to be getting better milage.
when i took the trannies out, i noticed the cranks seem to be entirely differnt (should have taken a picture) and the point where you would insert the pilot was about .5"+ sunken in on the zj compared to the xj, i went ahead and stuck the new pilot in anyways and hope the tranny imput shaft got in there at least a little, but i don't have any weird vibration, so seems good enough.:homer:
Good luck, i'll try to get up some pics, but i didn't take many :/