Sandy,
I am not familiar with re-staging, but it looks like the chemo has significantly reduced your tumor (or tumors) so the Tomotherapy can be more effectively.

I would imagine the radiation plan will closely follow the NCCN guidelines for cancer of the oropharynx - http://www.oralcancerfoundation.org/treatment/pdf/head-and-neck.pdf

Regardless of staging, the primary area normally gets the 70gy maximum as do involved levels of lymph nodes. I expect they will program the Tomo to 'paint' any areas where a tumor is, was, or might be. Some uninvolved levels of node will likely get 40-60gy.

It seems unusual to see your bio as stage III with nodes involved. I thought tht normally boosts it to a stage IV.