So I removed the pieces of dust boot flopping around inside the spring.... Made no difference. I'm now suspecting it's the ball joint on the UCA. I've ordered a replacement joint, and will have it replaced when I take the car into the shop to diagnose the problem.

 

Had a similar clunk after I replaced all the stuff you replaced. Also ended up being the balljoint on the UCA.

 

mine's fixed finally... I think it was more than 1 problem with my car


Caster arm bushing shot
tie rods started to lose some grease
ball joints started to lose some grease
passenger side wheel bearing shot (replaced both)

replaced sway bar bushings and the handling is better even though the bushings were decent..
LCA 1 bushings and UCA bushings were in ok shape..
Other things people might consider are either bad calipers/break pads and shot strut..

i think if the car has enough miles it just makes sense to replace all in one shot rather than trying to hunt the problem. if you decide the keep the car for long, it does make sense.

BTW, I had the timing belt changed at the dealer and got the 13 GS350 as a loaner (with 19 miles on it )... after all the suspension pieces were replaced, i think the 2g ride is comparable to the 4g ride (at least that's what the wife thinks. ).. 4g is not a bad car though...it was really spacious unlike the 3g and was definitely better than the newer 5 series or the A6 in terms of handling and power.. except that RWD beats AWD anyday.. i know what my next car will be now..

 

and also check the body brace.. it does rust a lot and the brace plate could come off as well as the exhaust pipe clamp that could rust and come off..