Hey there!
I can sympathize with your problem. I just got my car back today for the at exact problem. Although, this is the second time it has been in for the same thing. This time though, Lexus re-insulated the entire dashboard, console and all of the doors. The cracking sounds seems to be gone but, only time will tell.
One other you might want to be aware of is the that glove box apparently can allow items to fall behind it and into the air-door of the ventilation system. I only know this because a CD that was in the glove box escaped through the aforementioned air-door. It became lodged and susequently shredded by the blower fan blade. The only clue to what had happened was when I started the car, the sound of a baseball card caught your bike spokes could be heard immediately upon startup. They claimed to have fixed this problem and even gave me the chopped up CD. However, I started the car this evening and there it was again. So tomorrow, its back to Rallye.
On a side note...
If you have not done so already, there is bulletin out for Lexus to replace the brake pads.