I have a 2005 supercab fx4. It had what seems to be the exact same issue. I replaced the sway bar links (5k483) and the noise went away for 1 year. Now it is back. When I took the old ones off they seemed fine. however after replacing them anyway it cured the noise issue......I am looking for some sort of heavy duty aftermarket links.

 

I am pretty sure it's your upper control arm hitting your coils, especially if it is noticeable on rough roads. Look at your coils and check if any of the black coating on the coils show contact wear. I just installed a 1" DayStar on top of my lift and the the UCA looks pretty close to the coil. Having said that, AutoSpring recognized this to be an issue, that's why they came out with an "offset" version which creates more space between the coil and the UCA.
BTW, I cannot see this causing any serious damage but will limit down travel a small amount.