""Guys it's a "Truck" AWD off road vehicle. If you want a car base SUV get one of those Lexus mini vans RX330's.""
This has nothing to do with it being a "truck". Dozens of other truck manufacturers using slip yokes in their drivetrains do not have similar problems. Toyota has a design defect along with the lexus GX470. Look at the Lexus forum...they are replacing entire driveshafts!
Since it's not a safety related complaint, Toyota claims, "That's normal, they all do that"
There is no excuse for a $40,000 vehicle thumping every time you brake to a complete stop and release the brakes.
I do agree with your last point. If you like the vehicle it's something you have to live with unfortunately.
Update on my 2001: I just replaced the rear u-joint that attaches to the slip yoke assy. I'll let you know if there is any improvement.