I would take a close look at the anti-sway bar bushings where they mount to the frame/body. They could be worn allowing a deeper thud/clunk sound over bumps.
I'm sure there's a write-up on proper testing of these somewhere on the internet.
I know I'm coming in late to this post but I have the same clunking in my front end. It is the sway bar end ling bushings. How I figured it out with minimal work is I pushed side to side on the tires to shake the truck and when I heard the clunking, I would touch each of the components under there. I felt a thud on the sway bar every time I heard the clunk.