I don't have any advice about the bolts that hold the rotor to the hub, but another thought (possibility) came to my mind. The guide or track rod that attaches to the lower control arm (LCA)and runs to the firewall could be creating this noise also during braking.

You might especially feel the clunk at your feet on the floor during braking. The tapered bushings where the guide rod attaches to the LCA could be worn as well as the guide rod mount assembly at the firewall. I believe these items if worn would also transmit that same sound and feel.

My .02 cents worth.