I've had the clunk when starting and accelerating, BUT now in the pas week I've noticed that when I slow down for a stop light and my truck starts shifting down it clunks at a certain gear. Not sure but i Think its 3-2. By the way the clunk starting off or accelerating is rare.

 

There is a tsb for this, "Harsh 3-2 down shift". Fix is a pcm reflash.

 

ive had the same clunk since ive owned the truck. 20,000 miles later ive had it in the ford for numurous things and 3 of which is that stupid clunk. the sound is similar to the sound of bad u joints. anyways ford greases the slip yoke every time i go in. it will stop clunking for a month then it comes back. they did do the re flash once but that didnt matter because as soon as i get home i boot up the super chips. just fyi, i also had a clunking problem when turning. ford has a tsb for that too. they replaced the clutch packs. the two different clunks are unmistakeable.

 

Mine shifts rough from 1-2. Could a refalsh help this?