The axle part of the swap is actually very easy. Since the later models don't use a central vacuum disconnect, it's just a matter of installing the axle. Look for a high pinion axle from an earlier model as they afford a little more ground clearance than the common late model low pinion D30 and make sure it has no disconnect. If you're lucky you'll find the larger Dana Spicer 297 joints which are considerably stronger than the stock 260 joints. Look for an axle from a rig that had ABS and you may find them.
The last swap I was involved was a pre-'97 model so some of what you may experience may be a little different. That said, the 2WD models usually had access plates screwed into place under the carpet for the t-case shifter and the console needed only to have a plastic cover removed to provide access for the lever.
Choose the transfer case based on how you will use it. There were 2 available when your Jeep was built. A 242 allows full time 4WD on the highway and the 231 will give you a part-time case that allows you to upgrade to a 2 Low kit. This gives you rear wheel drive in low range....very nice on tight trails and on Moab slickrock. Make sure the t-case is compatible with your speedo output that should be on the tailshaft housing on the transmission. It will be moved to your t-case when the swap is complete. If the vehicle is lifted, or will be, consider doing a slip yoke eliminator now and using a CV style rear driveshaft.
The transmission is the only questionable piece as it might have an extension on the housing converting it to 2WD use that could be removed. I honestly don't know the answer to that. I would suggest posting the question on NAXJA.com or at my club's site,
www.PNWJeep.com.
After that, it should only be a matter of adding the correct drivelines.
If you want full functionality, you would want to investigate whether the wiring exists for adding the t-case to the system so the dash lights work. The lights may actually be there but just not connected. Personally, I wouldn't bother as you should be able to tell what drive mode you're in based on shifter position and input from the vehicle's behavior.
Hope this helps.
John