Thank you all for the replies. I tried easy stuff first. I checked under all the seats. I thought maybe it was the jack which is under the front passenger seat. It is not very tight and can wobble a bit. If I do it with force it makes a similar clunking sound. I stuffed a wadded up cloth between it and the floor to prevent that. Clunk still present.
It definitely comes from the rear. Today I tried getting in my truck and squatting/standing to bounce the bed. I can easily reproduce the sound while only making the bed drop an inch or so. The clunk comes from the driver side rear. While standing beside the truck, I can even just put my weight on my forearms laid on the side bed rail above the tire and bounce the truck enough to make the clunk. It makes distinct clunk if I do that on the driver side. If I do it on the passenger side, there isn't much of a clunk but there is sometimes a sharper clack sound from the driver side. I had my son bounce the bed while I was under the truck. I could not tell where it was coming from exactly but it seemed like it was well above me, so closer to the bed than axle. It seems like in the spring or shock. I can feel the clunk in both. When driving we all feel like we can feel it in the floor. I'm not sure what exactly to look for. Due to the fender liners, I can't see the top of the shock or spring very well. I think I'd have to take off the Bushwacker flares to remove the liners. Nothing is loose by hand while the vehicle's weight is on its tires. I have not jacked it up. The only jack I have is that one under the passenger seat.
Can a shock go bad and cause the clunk? Or, is it going to be a mount-point issue? The shocks are the Fox Performance ones you can add onto the Zone lift. The springs are the ones you get with the Zone lift. The lift was installed less than 10k miles ago. The truck has less than 45k miles total. The only time I've been off road was at my buddy's property where I have to drive up a driveway cut-in that is still just dirt. So, I have not been on anything rough.
Treat me like I'm ignorant, because I am on this stuff. I've never done any auto work. I replaced the brake light bulb above the cab last weekend and felt pretty proud of myself. Pictures would help a lot.