Hello Di x,
I checked the route that you have listed above and this is already the best possible route to visit each of the places that you'd like to make a stop at. A 21 day JR Pass is the way to go here, if you can use it to return to Tokyo by the day it expires.
A couple of other nice places you could consider:
Nagasaki: adding Nagasaki would mean a good amount of additional travel but this could be worth it. Nagasaki has a lot of history and is a very nice harbor town by itself. There is a great night view like: Mount Inasa and overall it is a very laid back city. You can also make a visit to Gunkakuji also known as battleship island. The best place to add it would be between Himeji and - Hiroshima. This way you would avoid doing Nagasaki - Kanazawa in one go.
Takayama A history (but quite touristy) village. Where you can see and experience how people used to live in the more remote parts of Japan. You can also make a side trip to Shirakawa-go from here.
Hagi this is a small history and slightly remote town north of Hiroshima. Hagi is very pleasant in that you can feel away from everything for a bit and enjoy some day dreaming about times past, before returning to the busy city life.
Onomichi Onomichi is a quiet harbor town (also) near Hiroshima. It is also a very pleasant town to walk around in, try to local Ramen shops and there are different beautiful temples in the close by mountains.
I recommend reading up on these places a little and see if they speak to your imagination. You'll definitely have enough time to include a couple with a 21 day JR Pass.
Hope this helps,
Daniel
