If it is making a "clunking" style noise to were it sounds like something is banging, its your struts not tightened. Double check your bushings inside the trunk and out under the wheel well.
The springs themselves don't really "settle" but its possible that your rings are sliding on around the knuckle. I'm not sure if D2 has fixed this issue or not since they never completely fixed my issue for the rear, but the rear perches for the springs are waaaayyyy too wide and big for the rear knuckle. (Assuming they haven't fixed this) The diameter of the upper rear knuckle is nearly 3 to 4 times smaller than the diameter of the top part of the rear spring. Every now and then, I have an issues where I can here this sliding, but its rare since my car is used to where it sits on the sprint now.
All in all, just go back and re-check everything. I know that it seems that you have checked everything, but trust me, I did the same thing before I found out what the heck it was and I didn't have anyone that had this issues before so I was all alone trying to find what it could be.
If you have any other questions, let me know. I'm a ghost on this site and I like to lurk quietly, but I'm a big wheels and suspension guy and do not mind helping anyone out!