Make sure your exhaust isn't hitting the body or other suspension components in the rear. It's easy to move the exhaust around on the hangers when installing or removing the rear springs. Plus, the exhaust hangers wear very easily and one could be torn.
You can also check the end-links too. Give everything a good wiggle back and forth to see if there's any contact. It's hard to diagnose this symptom without having the car in front of me, as there's a lot of components that could cause a clunk.
Let me know if you have any luck with this or if you have any other updates!