I imagine the first thing you should do (after giving your Jeep an affectionate pat on the withers for getting to 330 thousand miles) is to check the axle shaft u-joints. That's not hard to do. You can just reach into the knuckle where you can see the joints, and see if they are loose or rattle. If they are loose, you need new ones. Very badly worn axle u-joints can cause strange random pops and knocks, as strain causes them to wrap up and suddenly release. You'll also sometimes hear a jingling noise as you slow down to a stop. Someone else can give you the recommendation for upgrades. I usually just put in the stock ones because I don't wheel hard and in Vermont the salt mud and slush usually eat them up every 50 K or so anyway. If you can't feel play, you might also jack up each side and try rotating the wheel while cranking the steering to full lock. A good joint will not bind. While you have a wheel up, try yanking on it to check for wheel bearing and ball joint wear. The wheel bearings should be smooth and have no play at all (hub replaced as a unit). Badly worn wheel bearings will sometimes give you a scraping noise, especially on corners, but they can also clunk and pop. If you pull at 12 and 6 oclock on the wheel, you should get no movement, and if you do, your ball joints may be worn.
If you do underake the axle shafts, search the forum archives, and you'll find many hints and tricks on getting rusted, seized front hubs and the like apart.
All the joints in the driveshaft are also rebuildable, and you should be able to check that pretty much the same way. Play and binding bad, rattles bad. The front driveshaft has a double cardan joint with a ball in the middle that can make funny noises when it wears out.
Sometimes a worn control arm bushing or track rod can cause clunking too. At that age and mileage, the steering gear could also be worn, but many of these things would likely cause noise or problems in all conditions, not just in 4WD. Basically, you need to get underneath and start yanking and shaking and wiggling things, to see if you can find anything worn.
Finally, on an 89, there is a vacuum disconnect axle, and a fault in that system can cause clunking and popping if it is disengaging when it shouldn't. This will usually be a pretty pronounced clunk and a jerk, and may cause the 4WD light to blink off as well. It's more likely to happen when pulling hard, or as you're just cresting a hill, when engine vacuum goes low. Suspect this especially if the clunking is random or intermittent, and if it causes a perceptible jerk of the whole vehicle.
