From what I discovered and after talking to a few people at dealerships and performance shops, usually if there is a clunking noise coming from the suspension area that is has to do with the top side of the strut where it mounts to the strut tower. Open your hood and bounce the car up and down. If you see that one of your strut piston shafts and bushings seem to be moving around then somehting is not right (missing bushing, spacer, washer, bumpstop, etc.). When you bounce your car up and down there should be very little to NO movement from the struts piston shaft. If you here even the slightest noise when bouncing the car, it probably has to do with the top bushing area of the strut.

In my case, I was missing a bushing and spacer that had fallen out when reassembling the strut. This caused the struts piston shaft to just wobble around making a clunking sound. Also, did you cut your bump stops in half?