Habious,
When my car was making the noise, it would clunk just by my sitting down in the car first thing in the morning and I'm hardly a large man by any means of the definition! After the shop greased the clip guide (& whatever else they did), that noise went away. Mine was totally unrelated to the transmission. (It also made the clunk when reversing before the fix.)
So you may be able to rid yourself of the noise with one of the brake clip fixes.
Harold

 

The cause of this noise is the dry pivot points in the link that connects the left lower control arm to the automatic headlamp height sensor that is bolted to the left lower frame of the car behind the left wheel. The ball sockets dry out over time and creak/clunk upon sitting in the vehicle (lower control arm moves when you sit in vehicle).

The fix is replacing the pivot link (only available by buying whole sensor assy $450.00) or removing link gently prying back ball socket seals and forcing "Never Seize" graphite based grease into ball sockets. See my post "Clanging in L/f Suspension upon sitting into SC430". Good luck. My car is fixed!!!!!!!!!!!!!!!!!!!!!!!!!!

 

Tiglesias:
Last week, I had my Lexus mechanic in Charlotte do exactly the same procedure that you did; and, wham! Problem fixed! Charged me an hour's labor of $120 which is much better than the verified replacement price of $450. He was glad to do it and really happy it was the fix I've been chasing.
Many thanks again to you for posting this. I'm not able to DIY stuff, so, anyone else who can't and has this same noise, explain it to your tech and try this. If your height control sensor link boots are dry, this will fix it.
Happy!