Sunday we discovered the problem. It is the fit, or lack of fit, in the front floating rotors. By rocking the bike with the front brake on you can see and feel the movement where the inner, hub meets the outer ring of the disk. The rivets that keep the inner and outer together is too loose. The clunk seems to get even lounder when the rotor is hot.
This is the same thing I have discovered. Several have blamed it on the brake pads moving, but that is not the case. In my case it was the rotors moving slightly on the aluminum carriers. They moved almost 2mm when the bike was new. As I have put on miles, they seem to have seated themselves in some and don't move as much now.
I wonder if folks with new bikes are blaming the clunk on loose steering head bearings when that it not the source. When my bike was new, I could grasp my rotor from the side (like a steering wheel) and physical rotate it on the carrier and reproduce the exact sound I heard when riding. I haven't tried it lately as the noise seems to have subsided.