Finally got around to replacing the original struts on my 00 LE with 140k miles on it. The new KYB GR-2 struts installed easily as I had done the job on my 99 Solara a few years ago. Well before and after I have a thud thumping sound coming from the left rear strut tower although it is much louder now. I replaced the following parts so far:
[ul][*]struts KYB GR-2[/ul][ul][*]strut mounts (NAPA)
[/ul][ul][*]rear sway bar bushings
[/ul]
I pulled everything out of the trunk including the spare and jack and the noise continues. The noise is most noticeable at lower speeds over small to large bumps. I am really at a loss since almost all components that can contribute to the noise have been replaced. The upper mounts are NAPA brand and seemed a little cheap, just ordered KYB mounts from rockauto.com so we'll see. The only part not replaced yet but will be is the lower spring isolator bushing so I'll let everyone know what happens.

On a positive note the strut can be removed, disassembled and replaced in about 15 minutes now. [8D]

 

It sounds to me like it may be the LCA strut bushing, which goes bad with that mileage easily. Take a look at the bushing while your car is on the ground and if you need to, compare it to the other side, which isn't thumping just yet.

OR

Did you tighten everything to torque specs? Sometimes a suspension bolt that has been removed, replaced, removed, replaced... ...starts to get weaker and can't be tightened as much as it should.