Right Pass for Itinerary and Town suggestion

Hello,
We will be travelling by train from Tokyo to Hachinohe in October. The next day, we will walk (and take local trains) along the MCT to Miyako, 6 days later. Then we will travel to Morioka where we want to explore some of the nearby mountains and walks. After 2 to 4 days we will return to Tokyo by train. Finally we will travel over to the Kyoto/Osaka area, but will probably take some side trips in the general area. We are not sure about destinations yet. Twenty one days later, we fly out of Osaka. I am thinking that we will probably buy the 21 day National JR Pass, but I see that it may be cheaper to buy separate train tickets rather than the Pass. However for flexibility and convenience I think the 21 day Pass is better. Do you agree? Also, question #2, can you suggest one or two towns or smaller cities between Morioka and Tokyo, where we may use the JR trains (and Pass), and stop for a few days to enjoy the nature, Fall colours, walk, and maybe rent a bike for a leisurely to moderate bike ride? Thank you very much.