If it's still stock driveline, the OP's m1009 has a different setup than what you're describing. CUCV's all use a slip yoke style tailhousing, so there isn't a splined coupling in the driveshaft itself. If you want to get rid of it, you need to change out the T-case output shaft/tailhousing to a fixed yoke style or get a SYE kit and have a custom shaft built.I'm just getting educated in the CUCV world, but this complaint is a common one for owners of full size Broncos. The fix for Broncos is to lube the slip joint in the rear driveshaft. Although I've never seen a M1009 rear driveshaft, I imagine it's also a DC with a splined slip joint since both vehicles deal with a short wheelbase and a relatively steep rear driveline.
Anyway, there's one more thing to consider while your underneath checking bushings and mounts and what-not.
Good luck.
Note that on a M1008 or any 1 ton CUCV variant some "clunk" sounds at low speeds are totally normal because of the Detroit Locker in the rear. If you ever take one apart you'll see why it makes those noises when you suddenly let off the throttle at low speeds (engagement cogs need a few degrees of "slop" or lash to work as designed)
The M1009 uses a G80/Gov-lok rear "locker" which is a totally different setup than a Detroit Locker. It shouldn't really be making any noises - unless something's damaged. However, Gov-loks are well known for breaking parts. Maybe worth pulling the rear diff cover to check and see if everything looks intact? M1009's also use a NP208 transfer case which is well known for making clunk sounds if worn or sloppy. If you can rule out U-joints, my guess would be probably some kind of excessive lash problem at the rear diff, or at the T-case. The diff is relatively easy to check, but the t-case involves a lot of disassembly to check internals.