I have a 97 f150 4x4 5 speed manual with 103000 miles. I have a clunking rattle that happens over washboard style bumps while not on the gas or when clutch is pressed. Also seems to not do it if i engaged the 4x4.
The truck has new clutch, slave and master cylinder, sway bar links, tie rod ends inner and outer, lower ball joints, upper control arms, and shocks front and back.

 

Sway bar end links
Pitman arm
Idler arm

 

Sway bar links are new. The idler arm and pitman are still good. It seems to be when the rear hits the bumps.

 

Are you in the rust belt? Check the gas tank straps (recall)
Spare tire loose on the winch?

 

The clunking can be felt in the gear shifter. Spare not loose already checked that.

 

Check the u-joints, transmission mount, and motor mounts.

 

Visuals check of mount look good and cannot be move by my weight. U jount have been checked during clutch replacement.

 

It might be internal to the transmission and or transfer case. I have a lot of slack in mine. When in 4x4 it binds the system so it doesn't rattle. Off the gas or on the clutch releases any pressure on the driveline. I learned live with the noise...

 

is there the proper oil level in the transmission? or Tcase? Presumed you checked both front and rear U-joints

Have you checked the exhaust to make sure that it isn't loose?

How about the cab and truck bed mounts? Or something slid in between the cab and bed?