This is not a direct answer to your question but I would like to show you some thoughts.
First, you will travel for 14 days (plus 2 days in Tokyo?) and have 11 destinations which I think is too much.
Second, you will do some day trips, but it will take more time than just visit place A on the way to place B. Third, you don't mention when you will travel. If it's spring or summer you may consider night bus, for example from Shinjuku to Takayama, but in winter, the bus will arrive too early. Actually, operating date for this bus is from April 7 to November 4 for 2023.
Fourth you don't mention your traveling style. I strongly recommend you to travel with one "check in size" backpack, but this may not fit with your style.
I would just guess you are a young solo active traveller traveling in spring to summer and suggest an alternative itinerary.
Day 1 Night bus from Shinjuku to Takayama.
https://www.nouhibus.co.jp/highwaybus/shinjuku_en/Day 2 Explore Takayama and stay there.
Day 3 Bus to Shirakawago and then Kanazawa.
Day 4 Shinkansen to Tsuruga and then Thunderbird limited express to Shin-Osaka and then to Hiroshima (about 6 hours). Buy JR Kansai Hiroshima Area pass and use it from Tsuruga. You must disembark at Tsuruga to get the pass, but in any case you must transfer at Tsuruga from Shinkansen to Thunderbird. Stay 2 nights in Hiroshima.
Day 5. Explore Hiroshima and Miyajima.
Day 6. Hiroshima to Himeji (Himeji castle), Shin-Kobe (Nunobiki garden) and finally Nara (via Shin-Osaka). Stay Nara for 2 nights.
Day 7 Explore Nara.
Day 8. JR train to Kyoto. End of the JR Kansai Hiroshima Area pass. Stay Kyoto for 3 nights.
Day 9-10. Explore Kyoto.
Day 11 Shinkansen to Tokyo. I donft recommend Hakone, since your chance to see Mt Fuji in spring/summer season is rather low.
You will have 3 spare days. You may add 1 night at Kanazawa and Kyoto and visit Okuhida onsen close to Takayama 1 night.