I have been trying to locate the clunking noise in the left rear of my Bonneville for quite some time to no availl. I have read all the forums relateing to this, and have done the following;
1. New shocks (Monroe) noise still there
2. New upper shock mount. noise still there
3. Swapped the shock mounts from right to left. noise still there
4. Checked all bushings, they seem OK.

This clunking sound is only heard at low speed like driving through town when going over hard bumps like potholes or RR tracks. If I hit the same bumps at 50 mph there is no noise. Car is as quite as can be on the highway. It sounds as if its coming from the trunk area on the left. This is driving me crazy. Any Ideas

I am having the same problem! I finally took my 2000 SE into the dealer last week for them to check it out. They told me it is the intermediate shaft (steering). I dont understand because the noise is CLEARLY coming from the rear. I replaced the rear shocks and mounts 6 weeks ago. Same as your problem: low speeds only, medium to large bumps and potholes (except my noise sems to be coming from the center of the rear. She has 160K miles. Is there anybody out there with a solution?

I think I've got the fix for you. I've changed both rear wheel bearings and both rear shocks chasing this noise-not that they didn't need it anyways. The problem on my '01 SLE was the "adjuster links" which extend from the center of the car to control arm on each side of the car. The ball joint which attaches to the control arm had play in it. It was difficult to find as the play in the joint was not evident unless the car was sitting just right. If you jacked the rear to check things, it would change the position of the joint and it would feel tight. In my case only the passenger side was bad. ~$230 from dealer-you have to buy the whole link as it is a welded assembly. good luck. I Feel soooo much better this rattle is fixed.

I still need help with a LIM gasket replacement-just incase you've been there.

Haz

Kind of an old thread but I just wanted to say thank you. I have been throwing money at this problem since I bought my car a year ago and until I found this thread I couldn't find anyone who figured this out.
I read this thread to my mechanic and a couple bucks later the clunking was gone.

I'm glad we were able to help, even if it was indirectly.

And Just what was the exact fix??