We are well-familiar with Sedona. We have a place there, and we have been going there for 20 plus years. I would skip the Pink Jeep tour, personally.
It should be OK by then, but the town on the South Rim of the Grand Canyon had some serious flooding issues with a monsoon storm in August. We will actually be in Sedona October 17-26. Fantastic time of year.
I have a long e-mail that I send to people who go out and stay at our home that I can share with you if you message me off this board. I can't send a message as a free member.
For a hike, one of our favorites is the Chicken Point Loop, which you can pick up at the Mystic Trailhead. You can also check out the Chapel of the Holy Cross, which is built into the red rocks. It's about a 2 hour hike, 1.5 if you move more quickly. You will actually see the Pink Jeeps driving out to Chicken Point, but the hike is so much more fun.
At that time of year, our favorite hike is the West Fork trailhead. Not a difficult hike. You will cross small portions of Oak Creek several times, but the scenery and the leaves changing colors juxtaposed against the red rocks are spectacular.
There are so many places to see (and you said Prescott/Sedona)--definitely stop in the small mountain town of Jerome. Cool views, and a favorite restaurant of ours on the top of the mountain is The Asylum, a former hospital for people with psychological issues. It was on Ghost Hunters.