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Springs usually settle after only a few miles of hard driving - As little as 20 miles. So I'm told by Ray West who builds race cars etc and knows what he's talking about - He did my original suspension.
The trouble with clicks and clunks etc is that sound travels and it could be any number of things. Among other checks, check your anti-roll bar bushes, drop links, wishbone bushes.
Also make sure your coilover top mounts are well lubed.
Of course, as your car has only done 4k miles, I may be barking up the completely wrong tree!