As a owner of an 05 GX and a Lexus master tech, here is the unoffical word that I have gotten from the tech department---a revised rear driveshaft is still under development---I have worked on GX's 03-05 experiencing the clunk, and yes mine does it too---the problem lies with the slip yoke on the end of the driveshaft (end of the shaft slides in/out on splines)---the clunk comes from the splines that are machined onto the main part of the shaft and the yoke sticks as is slides---has to be at the right height to make it happen---first there was a service bulletin with an updated shaft---still makes noise with new shaft--then there is an un-offical field fix that involved cleaning/smoothing out the splines--50/50 chance if it worked---as of right now, when a GX comes in with a clunk complaint---we submit VIN and customer info to Lexus tech center and they are building a case for correction---still have yet to see new "updated" shaft (2nd time), but i will keep everyone posted--I have access to all Lexus service bulletins if needed (Lexus service bulletins are public type documents---there was some lawsuit that made it illegal to keep service bulletins from the public eye--if you go to a Lexus dealer and ask for a copy of a bulletin, they should give it to you hope this helps answer some questions
Jason