Strip out the clutch pedal, or just drop it to the floor - you won't be using it anymore.
OBD-II (1996-up) means you'll need a PCM from an AW4-equipped XJ, since they stopped using a secondary controller for OBD-II. So, got a donor vehicle? Or, order a reman.
I don't have my FSMs to hand, but I don't think there are any engine control wiring changes. However, you'll need wiring for the AW4 (it's electronically-shifted using solenoids.) The transmission throttle opening signal is internal to the PCM, so you should be fine there (once you change the PCM.)
You'll need an AW4 shifter assembly - I don't know what all will work, but I think it's cable operated - meaning you can use any of the "second generation XJ" shifters (1987-1996.) I think. The centre console should be the same - but you'll need the shifter bezel as well, and I don't know if it will fully cover the hole for the manual stirring stick.
You will need to carry the transfer case over, since the earlier ones are 21-spline (mid-1989 was the break.) Later units are 23-spline.
Make sure you get a flexplate (for your engine year, not the transmission. RENIX and OBD are different, but I don't know offhand about OBD-I and OBD-II. Just get one for a 1996) and a torque converter (should be the same 1987-2001. I've got one, but I'd have to drain it or plug it, and it's heavy to ship!) Flexplate-to-crankshaft screws are shorter, so you'll want to replace those as well (1/2"-20 x just over 1/2". The ones I used last time were ARP - a kit for Pontiac - the screws were 1/2"-20 x .590", methinks. Should be the same for you. Flywheel screws are about 3/4" long, and will try to "mill out" the block casting when they stick through the flange. Torque converter screws are, I think, M10-1.5 x 15m/m, or maybe 20m/m long.)
That's the quick thoughts, anyhow...
Why for do you want to do this, anyhow? Seems like a lot of work...