Today I finally got around to adjusting the alignment on the 4Runner (been meaning to tweak it as the steering was a bit off from center and it was annoying me) and noticed that my rear Cam Bolts were a bit loose (not flopping around loose, but enough that I didn't need to strong arm them to break them free.)
I can't 100% confirm it right now, but after I finished the alignment I torqued them to 120ft-lbs (FSM calls for 100ft-lbs, but I figured an extra 20ft-lbs wasn't going to hurt anything) and the clunk seemed to go away. Worth a shot if anyone wants to try it, I'll let you guys know if it comes back tomorrow.