I had the clunks you described. Lexus replaced the struts, mounts, and performed a TSB for that noise on it. I still had the noise....
It turns out my '99 RX300 had a bad wiper motor bushing that caused the motor to creak/groan/squeak when the vehicle went over bumps at low speed, especially while turning over a bump at low speeds.
I know it sounds crazy, but my neighbor had this done on their '99 RX300 as well. When the chassis flexes, this bad wiper motor bushing did not insulate the motor which caused the motor to rub and/or clunk against it's mount.
My Lexus dealership said they see it from time to time.
Changing the wiper motor bushing absolutely fixed the problem.
I now have an '04 RX330 and like many of us now am sorting out the gremlins.
Jonathan