Five months later, have you guys found any resolution to this problem? I certainly hope so, as I have the exact same thing happening and it's driving me insane.
A healthy clunk from seemingly right under my left footwell at low speeds, while applying or releasing the brakes with the wheel turned more than 1/4 travel to the right. It can be felt slightly through the brake pedal itself, though I believe it's just passing along the shock from the frame/suspension. Also get it when releasing the brakes in reverse, regardless of wheel direction. Similar noise when going over washboards or rought terran. In the course of my investigation, I found that the noise can be replicated with modulation of the throttle while in 4HI. Looking at the wheel as the noise occurs, it seems to shudder, just a degree or two of wobble associated with the clunk.
It's not the known cab mount nor the bumper mount issue. I've pulled the wheel off, I've checked every piece of hardware in the wheel well (left front), it's not the skidplate (pulled those off today, hoping). I've taken a rubber mallet and just banged on stuff but was unable to replicate the noise. I even rotated the tires, not that it was likely to help. FWIW, mine's an '06 DC TRD Off-Road, 3" Revtek. Stock tires, for now - I'd like to fix the present issues beore creating new ones. The alignment is fine, tires in balance. About 14k miles, but it's been doing this for at least the last 5k, if not longer.
As an aside, I did find the source of a tiny creaking noise by accident. A brake-line bracket sits on the aft part of the upper A-Arm. It appears that the current alignment had the A-Arm sitting rather far forward. such that the bracket on the arm rubbed against the coil spring. I pulled the brakcet, ground it down, and now it doesn't rub. Now as I write this I have to wonder, is there a connection with the first issue relating to the upper A-Arm being way forward in its adjustment? Is it ever even supposed to move?