One problem related to clunking noise has been reported for the 2000 Ford F-250. The most recently reported issues are listed below.
Was driving and applied the brakes, pedal started to chatter. Stopping distance was diminished. Took to dealership and was informed that rotors were warped. Was not under warranty for repairs. Electrical crossed wires in alternator system were smoldering. It was repaired. Front end would make clunking noise while turning. Nothing was found.