One of the mechanics at the dealer where I bought the truck found a TSB that seems to have worked to get rid of the clunk. I found some info on another site and am including it here.
Here is the TSB---real easy repair--you can do this yourself---works for a while. Basically the slip yoke is sticking and then pops loose and you hear/feel a clunk.
FORD: 1998-2004 F-150
Some 1998-2004 F-150 4X4 vehicles with a one piece drive shaft may exhibit a clunking or grunting noise and/or a shudder sensation from the driveline. The condition will typically occur during light to moderate acceleration from a stop and/or braking. This may be caused by the slip yoke not sliding smoothly on the transfer case output shaft splines.
To service, lubricate the slip yoke with Teflon Grease (D2AZ-19590-A). Refer to the following Service Procedure.
Road test the vehicle to verify the condition.
Remove the driveshaft per Section 205-01 of the Workshop Manual.
NOTE: INDEX (MARK) THE DRIVESHAFT YOKE TO AXLE FLANGE FOR REASSEMBLY.
Lubricate the slip yoke with 7-13 grams (0.25-0.46 oz.) Of Teflon Grease (D2AZ-19590-A).
Re-index and reinstall the driveshaft per Workshop Manual.
Check the transfer case fluid level and add MERCON Automatic Transmission Fluid XT-2-QDX if necessary.
Road test to verify the condition is corrected.
Saturday, April 22nd, 2006 AT 10:12 PM