7/8 of 21 day itinerary

I am busy planning my first 21 days in Japan.
The first part I have already booked: Hakone/climb Mt Fuji/Nagoya + 3 full days Kyoto
The last 5 or 6 days I would like to stay in the Tokyo Area
The middle part is undecided yet (based on the last 6 days in Tokyo area)

I have a 21 days JP railroad ticket
My main interests
food/onsen/nature/culture/cycling and maybe some local activaties (fruit harvesting/cooking/..)

My idea
1) Kyoto Nara Osaka
2) Osaka Miyajima
3) Miyajima Nagasaki 
4) Nagasaki  Hiroshima
5) Hiroshima Himeji Kanazawa
6) Kanazawa Takayama
7) Takayama Tokyo

Any suggestions about where to stay/go to instead are appreciated.
Thanks
Jeroen

To maximize the use of the JR Pass (or even to make it pay) you would want to do some long-distance trips! You might want to decide on your general itinerary before you decide on the purchase of nationwide JR Pass...

I would think the plan is already written there.
Question would be which airports are you flying into and out of Japan.
A second would be why Miyajima and Hiroshima on different days? They are close by and should be done together. Don't visit Hiroshima just to break the journey.

I already bought/have a 21 days pass. I don't mind if it is not 100% break even. I arrive and leave at Tokyo airport.
The break in Hiroshima is on purpose : Nagasaki to Kanazawa is 8+ hr. I thought it was too much of travelling for one day.