Yep. I would start with the motor.
Very first thing I would do is start with the oil pressure. The AMC engines are notorious for the oil pump getting worn out over the years. That means low oil pressure, which is "bad". And by "bad" I mean, it's not entirely uncommon for low oil pressure to cause starvation to the rod journals on the rear two pistons (#7/#8). That leads to bearing failure and throwing a rod. And that's a "you need a new engine" conversation. So check the oil pressure and make sure it's still good. If not, you may want to check the bearings for wear. And if you are going to replace the two piece rear main seal (a common leak source), you can check bearings while you have the oil pan off.
One note to a Ford guy. AMC numbers its pistons like a Chevy, which is different than the way Ford numbers them. Driver front is #1, and it goes #3, #5, and #7 down the drivers side. #2, #4, #6, and #8 go front to back on the passenger side.
BJ's Offroad is as good a place as any to find replacement parts.
http://www.bjsoffroad.com
Team Grand Wagoneer has parts but their shipping times and customer service aren't the best.
http://www.teamgrandwagoneer.com
There may be other places to find parts. There were some other AMC specialty shops but at least one of them has let their AMC parts business suffer substantially in the last several years and I don't even bother with them any more.
BJ's has an oil pump rebuild kit that's pretty easy to install without doing anything more than pulling a couple of bolts. They also offer a "mid plate" that puts a steel liner between the oil pump gears and the bottom of the aluminum housing (one of the places that wears substantially).
Getting a carburetor set up to run right isn't rocket surgery but it does require some effort. Having a vacuum gauge really helps getting it dialed in. As an alternative, Holley now offers the Sniper 2300 throttle body fuel injection system. It bolts right up in place of the factory carburetor so you don't have to do major engine surgery to get it installed. People seem to be having good luck with it.
Beyond that, the transmission (Chrysler TF727 with AMC specific bellhousing) is durable and usually not much of a source of problems besides possible leaks. The transfer case (NP229) is reasonably durable. The vacuum shifter can sometimes need new vacuum lines to get it to work right. And there's always seals that eventually start to leak on a 30 year old vehicle. A common saying about Jeeps: "If there ain't no oil under 'em, there ain't no oil in 'em."
It would be a good idea to check the frame where the fuel tank sits up against it. That's a common place for hard-to-find rust. It's not terribly hard to patch though if you can weld or find someone who can. Body panels can be patched easily enough by a competent body guy and you can find some replacement panels to make that job easier.
You can get new carpet pretty easily. And seats are easy to recover. Some interior pieces can be replaced with new parts. Others will require searching the For Sale section of forums like this and IFSJA.
http://www.ifsja.org
Also, the Haynes manual for the Grand Wagoneer is actually useful. You may need to order one online but unlike some of the other Haynes manuals, they did a good job putting this one together. It's no factory service manual but it has almost everything you need for most tasks.
Finally, upgrading the ignition is pretty easy. AMC used Ford parts in its ignition and upgrading to the TFI coil is only a few bucks more than replacing plugs and wires during a tuneup. Here is my write up on how to do it:
http://www.grimmjeeper.com/TruckNorris/tfi.html