My truck and another 99 2wd 4.6 auto that I've ridden in, both have the same clunk. It occurs when cruising at precisely 60 km/h and let off the gas pedal. It feels as if the truck is holding a gear (3rd?) longer than it should and when I let off the gas pedal I hear/feel this clunk (somewhat like a torque converter unlocking, but firmer) and feel very slight engine braking. I had heard that Ford revised shifting progams for the 99's to help them cope better under load, so maybe this is what I'm noticing.
Has anyone else noticed this and is it normal?

 

I have a 98 F150 SC 4.6, 4x4, same clunk, normal as told to me by dealers mechanic.

 

W1
Just out of curiousity, I dissconnected the battery for about an hour then reconnected and drove as per the manuals instructions.
And voila! no more clunk! In addition it feels as though the truck is a little peppier
than before and shift timing is also much improved. I am not hallucinating, I guess my computer never had the chance to "learn" properly on its way from the factory to the dealer.

 

I'll try it out and let you know if it works for me.