Service Update
Ok, I got the 4Runner back from service. Here's the update...
When I took it in, I rode with a tech to show him the problem. During the test ride, it only clunked once, and not too badly, but the tech told me he felt it. During the test ride, I showed the tech some papers I brought with me. I showed him the Lexus GX470 clunk TSB, as well as pages of complaints from this website and others about the clunking. He said he had never seen the Lexus TSB and would show it to his manager.
I tried showing the same stuff to my service writer, but he acted like he was Superman and it was Kryptonite. He told me, "all we do is lube the driveshaft and that always fixes it." I told him about the complaints that the problem comes back prematurely, but he changed the subject.
So when I picked up the truck, I got a copy of the service writeup. On this paper, they claimed the clunking noise wasn't duplicated (even though the tech claimed otherwise), but they lubed the driveshaft. My other complaints (concerning a squeak in the dash and another in the rear seat) were also dismissed with "could not duplicate problem." I even brought a copy of the rear seat squeak TSB to help speed up the process. No dice... still squeaks because they didn't do it.
So far, with the new lube on the driveshaft, that issue seems okay. I'm not surprised at all that Toyota didn't do more. They have their procedures and policies that keep them from doing whatever the customer wants. With that in mind, I am going to be paying attention to the clunk and take it in as soon as it returns. If that happens to be before my next oil change, then I'm gonna raise hell. Any REGULAR maintenance is not something you need to do more than once every 5,000 miles or so. If they expect me to crawl under the truck with a grease gun, they're crazy. So I'm gonna bug them with the issue over and over until it's documented enough that I can complain and push for the Lexus TSB.
In the meantime, I'll be providing feedback about my service experience to the President of the dealership. I met him last year and he's a decent guy who cares about his dealership's reputation. If he makes things right, I'll let you know. It doesn't look like a TSB is coming from Toyota anytime soon. Maybe they'll address the issue in the next gen 4Runner?