It could be your rear body mount (although my 1" BL has never made any noise), but that seems unlikely to me since the noise came back so quickly after you tightened the bolt. Makes me wonder if that was the issue or if it just happened to not clunk on the first bumps you tried it on. I've found that noises just love to disappear right after you mess with something unrelated and just when you think you figured it out, the noise is back, DOH!
Did you check the body bolt to see if it was loose again after the noise came back? Did you check the bolt on the other side? I'm thinking if you cranked down on one, it could have loosened another. But all that aside, I doubt it's your body lift because I've never had any noise with mine and I've personally never heard anyone having that issue on a 3rd gen at least.
So...
I would put one of your feet on top of a rear tire and sorta move your body back and forth so it rocks the truck. Have a buddy lay under the truck and listen. Or better yet, you listen and have your buddy rock the truck. I mention this "put your foot on the tire" technique because it works better than jumping up and down or rocking the truck with your hands because the motion is coming from the tire like it would naturally - as opposed to rocking the body with the motion coming from above. Find a spot where it will make the noise when you drive pretty slow. Then have your buddy stand next to the bumps so he can try to make sure that it's coming from the rear. Sound can bounce around down there and it's hard to know for sure when you're inside the truck.
Look at the panhard bolts and the bushings too. Just the other day, Driffter33 and I found his clunk with the way I described and it was the panhard bushings/mounts.