I had this same clunking issue about a year ago so I changed my front pads/calipers/rotors/wheel bearings and it went away. Fast forward to this last month and the clunking has returned. I hear the clunking while braking when decelerating at less than 40mph. I have provided a video to explain what's happening. Its coming from the drivers side and It gives me tactile feedback in the floor as well. From the outside, I can hear a clicking sound that kind of alternates with the clunk. Like CLUNK click CLUNK click. What could I do to remedy this?

Edit: jeep is a 1999 2wd

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Check your U-joints, and check your rear brakes.

 

I don't have u joints in the front (2wd) so could it be the driveshaft? And what do I look for in the rear?

 

Park the Jeep. Turn it off. Lie down next to the car, about half way back, grab the drive shaft. Wiggle the heck out of it. Hard!

It shouldn't move. Use two hands. Hard!

Wiggle up down left right. All over. The wiggle should come from the ujoint area if it's bad.

Gloves help.

 

Did this exactly. Wiggled it both in neutral and in park. No play from the differential side but there was play on the transmission side. The movement seemed to be coming from where the yoke inserts into the transmission, rather than from the U-joint. Could it be the race/seal on the extension even if it isn't leaking? I also discovered that there are segments of the rear wheel's rotation where it binds :/ I don't want to tear anything down until I have parts on hand either.

Heres what I did. Transmission is in neutral here.

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To determine if it's the u joint or the input shaft play, grab both yokes and try to move them then. That'll be checking only the u joint

 

I had the exact same thing, it was the spider gears in the rear differential. Also had a blown shock but the spider gears cleared up 98% of the clunk. And it only happened when I braked or was going fast and let off the gas pedal.

 

How old are your u joints? If they are factory original, I would just swap them out so you a) know they are new and b) eliminate the u joints as the source of the issue

 

^ they were replaced in 2008.

I did a brake adjustment by pulling the emergency brake while I'm reverse and also braking hard while in reverse. So far the clunk has gone away. Will report back after changing all the hardware. Also! Are the rears wheels supposed to bind at a certain part of the rotation? For example. If I spin the wheel by hand while off the ground, there's about 80 degrees of rotation where it's harder to turn. It happens on both wheels. Is it normal?

 

Did you ever find out what it was?