There should be so many options to complete your itinerary, so I will write just one option.
Buy Kansai Hiroshima Area Pass (13,500) and use it for 09/09 to 13/09.
https://www.westjr.co.jp/global/en/ticket/pass/kansai_hiroshima/To go to Tokushima, the fastest way is to take highway bus which is of course not included in the pass.
http://www.jr-shikoku.co.jp/bus/global/en/route/awa_ex_osaka.htmlReservation
https://www.kousokubus.net/JpnBus/enTo go to Kanazawa from Kyoto, buy normal ticket (6,900 yen for non-reserved seat).
From Kanazawa, buy Mitsuboshi Route Shinjuku ticket.
https://www.bus-navi.com/news/d3537db208ce9dcd2aff.pdfYou can go to Shirakawago, Takayama, Hirayu onsen (transfer to Kamikochi, additional 2,050 yen round trip), Matsumoto and then Shinjuku (in Tokyo). The validity period is 7 consecutive days.
So the total cost is: 3,700 (bus to Tokushima from Osaka) + 2,640 (JR limited express non reserved seat from Tokushima to Takamatsu) + 13,500 + 6,900 + 8,560 = 32,660 yen.
With this option you will have some flexibility for the traveling time. For example you can stay longer in Kyoto without worrying about the validity period of Japan rail pass. In addition this would be cheaper than 14 days JR pass plus some bus ticket.
Other comments.
Try to avoid Saturdays on busy place such as Kyoto, Osaka and Kyoto.
Why do you include Tokushima? Personally, I think Himeji, Okayama, Takamatsu are more interesting. If you omit Tokushima you will save some money.
Your itinerary it too gTokyo-orientedh. Try to allocate less for Tokyo and more for Kyoto, some smaller cities (Kanazawa and Matsumoto for example) and rural areas such as Kamikochi.