About the clunking, maybe it is a frame member that is flexing and popping? If a car is on an uneven pavement, ie entering a sloped driveway at an angle, at the point the front 2 tires are on the driveway and the read 2 are still on the street, there is alot of frame stresses, and the whole car twists. It is possible that one stmaped frame member connecting other structural points in the car is flexing and making the noise. I noticed this in my 2003 Honda element, not the noise but the frame flexing. I was parked in such a way described earlier, and when i opened and tried closing the rear hatch, it totally didn't line up until i pulled the car back onto flat ground.
just a thought.
because if you replaced the ball joints, lower A arms, there aint many more things that can generate such a noise. I guess could also be the steering linkage, loose struts, sway bars, etc... Let us know if the cause is ever discovered.