Does it do it every shift? Check the lash in the rear end. What I think may be happening is with stock shifting being so drawn out and soft compared to with the TranZsformer, with it the quick firm shift actually makes the car "lunge" forward, loading rear end lash, then after the shift, it unloads the rear end lash and you get a clunk. It's common on a rear end with too much gear lash. Also common for it to happen when going from park to reverse. Either to much lash, or a faulty u-joint.
