I've had varying clunks from my diff... I had whiteline adjustable top trailing arms that shagged the thread so that between the frame and diff there was an immense amount of play, thus a clunk. Also I have a TRD 2-way which makes some noise, but it has always done this.
If it is on hard throttle or even highway speed throttle blips and clunks, I'd check all you trailing arms and bushes and while the car is up check the backlash. Even with the wheel on you should be able to tell if there's a problem.