Well, I took the GX in this morning. Had a new to me service writer who understood everything about the clunk, and wrote up the service order for new driveshaft and control arms. Picked it up about 8 hours later, and it finally drives like a Lexus should.
Other problem was the sunroof. The auto open and close feature to the switch had quit working. Also, the automatic position changing of the wind deflector had quit as well. Neither the service writer or the tech who worked on the car knew the wind deflector had this feature, and it took a trip to the owner's manual to make it clear. Seems the wind deflector feature is tied into the switch, and reprogramming the switch solved both problems.
Finally, evething that was a problem with the vehicle at delivery 34,000 miles ago is resolved. The rear AC problem took 25,000 miles, and the tire inflation indicator light problem took 20,000 miles to solve.
I honestly don't think I'll ever buy another Lexus. I'll likely go back to BMW. I've had good experiences with my local bimmer dealer, from whom I bought an 86 5-series 20 years ago. It has 225,000 miles and is still going strong. It required a new driveshaft after only 195,000 miles!