Sorry....very late to the party.
I have the same issue. Turns out on my car, the rear swaybar bushing has worn. If you haven't figured your issue out yet, try inspecting the rear swaybar bushing and replacing if required.
I think the liner was replaced by the body shop, but i'm not sure. I did not notice it looking like it would be interfering when i first looked at the car, but I will definitely check that again.
I had the same thing - clunking on every bump. In my case it was a broken spring on the right rear, about 1/2 inch shorter than the other side as it collapsed one winding. Then the sway bar made up for it by trying to hold the car up. Still not sure what the actual source of the noise was, but I replaced the sway bar bushings first, with no results. Now after I replaced everything the noise is gone.
When inspecting my old rear suspension parts, all I could find was that broken spring. Downlinks were fine, bolts were all tight, and the shocks appear fine. Springs were old and crappy and stiff, but the same was true in the front where there was no rattle. Nothing was rubbing, as it only took tiny bumps to make it rattle, while it didn't clunk when loading up that corner of the suspension in a faster turn. I guess that when the car was neutral, there was some gap in that corner that would collapse and hit, but when compressing the spring further, nothing would rattle any longer.
Probably not what you have, especially after taking the shock out to inspect it. A broken spring would be quite obvious.
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