I officially hate you (not really... :tongue1

... I have been trying to find a way to get my extended warranty to honor the TSB even though its technically out of "factory warranty" according to the TSB (yet the TSB came out last summer and pretty much blatantly ruled out half the 4th gens without even bothering to extend the warranty period since it expired in like '08 according to the TSB :mad2
I don't know the situation you have with your clunk but from early on, the service manager and local/regional Toyota reps have known about the issue in general and my experience. I never bugged the service manager and we did on occasion talk about what was going on.
My assumption was that Toyota covered the 'fix' under my extended warranty with the TSB adding additional 'credence' to the factory covering the fix. I never asked the manager who was covering what.
The clunk is still 'quiet' but I need to say... I didn't authorize the technician to cut my accelerator pedal to satisfy Toyota's lawyers! They freakin cut it anyway while it was in for the replacement of the driveshaft.
After they cut the pedal, I told the service manager that the service advisor should have 'advised' me re: to sign a waiver and leave the pedal alone. They never did that!
The service manager then immediately ordered me a new replacement for the butchered accelerator pedal. I hate the replacement as well and I told 'em that I want an original accelerator pedal installed.
They're looking (I won't hold my breath) for an original accelerator pedal when one of the 4th gen 4Runners are being traded in and need to have the pedal replaced anyway. Again, I'm not holding my breath.
So, yes... I got the clunk fixed and I believe you might be able to as well.
And definitely, DO NOT have them butcher your accelerator pedal to satisfy the lawyers when there wasn't a problem to begin with.