This looks like a TJ with a D44, but the XJ should be similar (the XJ will have a longer driveshaft). You can see the rubber boot behind the transfer case. the yoke directly behind that boot slides forward and backward but you can't get access to the transfer case output shaft without taking off the driveshaft.

 

There are plenty of other things to check for rear end thunking.

As someone mentioned, shock mounts (the top bolts break all the time and a lazy P.O. may have simply omitted bolts), leaf spring bushings, sway bar bushings, rear brakes, rear end issues... you really have to look at everything.

 

Oh, thank you. I'm new to all of this and I've actually learned a lot since I bought it last winter. I'll take a look!

 

How were the u-joints on the driveshaft? I'm assuming they were tight as you probably would have noticed when you had the shaft off if they were not.

Look at the spring bushings and spring condition. When I replaced my leaf springs the driver's side literally separated in my hand as I was pulling the front side out of the bracket -- scary. I wasn't even getting driveability issues, I was replacing them because the springs were just super saggy.

 

The u joints seemed fine, I'm far from an expert but i think I'd have noticed if they were in bad shape. I bought the jeep with about a 3-4 inch lift and I've replaced a bunch of things already. All of the brakes on the vehicle including all brake lines and rubber lines are brand new, new track bar, sway bar link ends,... the suspension prob needs work, I know it def can use some love as it stands but when I have a moment I'll take a look at what you said to. Theres no rust or rot on the vehicle but the lift is def older. The components do look old and rusty. Looks like I have skyjackers and looks like rustys components but it's so old and crap, I'm not 100% sure about it all. I bought my 00 xj last winter and have slowly tried making it right. It's a cool little project though. It's the first time I've had a 3rd vehicle so it doesnt matter if I stop mid project and come back later, you know?

 

I hear you - my 95 is a second vehicle (my wife only drives in the rarest of circumstances) and I'd never be able to get away with having a 23 year old, previously owned Jeep as my primary vehicle. In the past I had a TJ that started getting a lot of problems and it was stressful dealing with stuff when it was my daily driver. With my XJ I can take my time - however the more stuff that gets fixed, the more I drive it and now I'm at the point where if I can't drive it, I'm not happy. I should'a remembered I have a Jeep addiction.

With a 3-4 inch lift, what was done to correct the rear end geometry? Typically folks go with a SYE (slip yoke eliminator) and C/V style shaft (like the front driveshaft) or lower the transfer case.
If the lift was poorly done or left the driveshaft angles incorrect (in other words, running the stock setup without lowering the TC), it can cause excessive wear. I wouldn't be all that surprised if the thunk is due to an issue with the differential stuff or pinion.

I'd start with the components and make sure everything is in good shape and go from there. It's much more likely to be something worn or loose than diff issues.

 

crap, well now I'm not sure. I'm trying to learn as I go so I have no clue what's been done really the guy I got it from didnt know much because he had bought it the way it was and I bought it because it was 1500 and always wanted one so ... I guess I'll try and figure out what's going on there. I'd bet its bone stock in that dept.

 

I'm not trying to scare you or anything.
If the driveshaft looked like a longer version of the picture I posted and it slid on/off as I described, then it's not a SYE.
If you look at the crossmember and it's flush up against the frame rail without any spacers, then there's no Transfer case drop.

I -think- that in order to get to 3 or more inches of lift, you have to use "lifted" springs, so likely the leaf springs are not original. Look at the spot where the spring touches the axle, there are spacers that increase rear lift, the OEM setup has the spring directly on the axle - there's a flat spot that's part of the axle housing. The other way that rear lift is achieved is with longer shackles (the part that sits at the back of the spring that connects the spring to the frame).

Since all the stuff in the rear end would have been taken apart to put a lift in, it would be a good idea to grab your torque wrench and make sure all the bolts are tightened to spec. These would be - the big bolts where the spring connects to the frame rail brackets, the bolt between the shackle and spring, the nuts on the U-bolts (the bolts holding the spring to the axle), the bolts on the rear sway bar (IF you have one, it's common to simply remove it entirely - if it's there, it connects to the top of the plate on top of the spring where the U-bolts are.. it actually uses the u-bolt nuts to hold the link on), the rear shock bolts and probably something I'm forgetting.

 

Here's some pics. Def dont have the sye

 

Idt my pics are uploading

 

You have a small spacer under the leaf springs - the thing that looks like a sanding block.

If you grab the pinion yoke (where the rear shaft connects to axle) and push it, does it move up/down or in-out at all? If you can move it at all by hand then it's bad.

Another thought - if you grab and shake the tailpipe, does it knock on the crossmember? could be as simple as the pipe hitting the crossmember (usually due to bad tranny mount)