Pulling an FC engine might be tricky (I haven't done it in an FC yet.) But pulling a transmission is just as with any other Willys Utility Vehicle. Pull it from underneath.
Park on a concrete floor, block the wheels, support the engine, remove all the linkages and drive shafts, put a floor jack under the crossmember (E-mail me for my Third-World method of doing this), remove the four bellhousing to trans. bolts, then lower the jack slightly and support the engine just below normal but don't strain the front engine mounts (This makes it easier to install), now slide the transmission to the rear while on the floor jack or trans. jack, lower it to the ground and slide it to the side of the truck for inspection. Get help from a friend when separating it from the engine.
With the transmission out of the way and ready for inspection, unbolt the bellhousing and remove the clutch. Check the condition of the flywheel. It would be best to have it surfaced. Check the wear on the pilot bushing in the crankshaft (grease slightly before installation, and grease the tip of the input shaft, too. I always replace pilot bushings while I have it apart), Bolt on the new clutch, tightening in sequence, and use an alignment tool to match up the clutch disk, making sure the disk is not on backwards.
After pulling the transmission, open the top cover. What is the condition of the fluid? What is the condition of the teeth? What is the condition of the brass synchro rings? What is the condition of the synchro rings on second gear?
I'd rebuild the transmission while it's out. It's easy, just follow the repair manual. The parts are around $250. Replace second gear, and install a small parts kit. The bearings may still be good. You can clean them and inspect them for pitting. Replacing them would be better insurance.
Transfer cases don't wear out as often as the T-90, where second gear doesn't last long. The intermediate shaft is what wears out first on Jeep Transfer Cases. You'll have to decide whether or not you want to do a rebuild on the transfer case, too.
When buying a new clutch, always buy a new pilot bushing and throwout bearing.
I always replace any wearing parts while I'm in there. I've only gambled and lost.