I don't know if this will help or not, but I think you should have a close look at the rear sway bar.
About 2001 we had a new Cougar in the shop with a rear end clunk that defied finding. Calling the Ford hot line I was told to completely remove the rear sway bar and road test the car. Sure enough, the noise was gone.
On further inspection, we determined that one of the sway bar bushing mount clamps was deformed. New clamps and bushings solved the problem.
