In my opinion I wouldn't perform the Lexus TSB. If you research the TSB it appears that they are using a teflon coated drive shaft so that when it unbinds it will slip with less noise. In the owners manual for the 4runner it clearly states to lube the driveshaft during the maintenance intervals...
I had the same problem. After joining this forum I learned that the noise was coming from the rear drive shaft. When the vehichle comes to a stop the drive shaft is bound and when you let your foot off the brake it un-binds and there for the "clunk". I took it to the dealer and they said it was...