I recently purchased a 2001 F150 4x4 w/ 5.4 L V8 Triton motor. It has 92,000 miles, and runs strong. The only problem I have noticed, is that when I put it in reverse I get a clunking noise, only for a moment, then reverse works fine (even with a boat attached). It is an automatic. The sound seems to be coming from the rear end. I'm not sure if it is the transmission, u-joint, drive shaft, or ring & pinion. Any suggestions would be appreciated.

Thanks

 

Coutranld be a couple of things, I would definately look at the u-joints and the transfer case tail shaft. Is there any kind of a lift kit on the truck? If yes, the U-joints could be the culprit and is the cheap fix. If you take the driveshaft off check the tail shaft of the transfer case and see if it has excessive play.
My 2004 FX4 had a technical bulletin on it for a clunking noise coming from the rear end and I believe that is was the U-joints also.

my .02 cents worth, hope this helps!