Optimized regional passes and attractions?

Hello,

My itinerary is as follow:

Day Activity Night in
D1 -4 Tokyo - 4 days Tokyo (5)
D5 - 7 Hakone - 3 days Hakone (3)
D8 Kamakura Tokyo (1)
D9-10 Nikko - 2 days Nikko (2)
D11 Matsumoto - 1 day Matsumoto (1)
D12 - 14 Kamikochi - 3 days Mountain huts (2)
D15 - 16 Takayama - 2 days Takayama (3)
D17 Shirakawa-go (no overnight) Kanazawa
D18 - 19 Kanazawa - 2 days Kanazawa (3)
D20 -25 Kyoto - 6 days Kyoto (6)
D26 - 28 Hiroshima - 3 days (daytrip to Miyajima Island) Hiroshima (3)
D29 Okayama Okayama (1)
D30 Himeji castle (no overnight) Osaka (1)
D31-32 Koyosan - 2 days Koyasan (2)
D33 Transport to Kumano Kodo Kii-Tanabe (1)
D34 - 37 Kumano Kodo Nakahechi - 4 days Kii peninsula (4)
D38-40 Osaka - 3 days (daytrip to Nara) Osaka (3)

I struggle a bit to understand how to optimise the transport passes since I will stay each time a few days in each destination.

I know there is a 2 and 3 days Hakone pass and a 2 days Hakone and Kamakura pass, but how to get the most of it if I stay 3 days in Hakone and 1 in Kamakura (meaning I always only get to use a single way from or towards Tokyo) and is it even worth it?

Same question for the Nikko pass: is it worth it if I only get a one way transport from Tokyo.

What other regional passes are worth checking? All the passes seem to be aimed at travellers with a very fast pace making it difficult for me to see if there is any of those that could serve me.

My second question is about the main attractions that would need advance bookings.

I had in mind so far:
- Toyosu Market tuna auction (Tokyo): the lottery system seems to have stopped in March. Can we still see it?
- Ghibli Museum (Tokyo)
- Digital Art Museum TeamLab Planets (Tokyo)
- Imperial palace (Tokyo) - is this one worth it or is seeing the part open to everyone most likely enough?
- Kokedera - Moss Temple (Kyoto)
- Hiroshima Peace Memorial Museum (Hiroshima)

Any thing I am missing from the list?

Thanks in advance to all for sharing your experience. :)

Best regards,

Maïté

Tokyo=4 Days
Hakone =3 days
Total=7 Days

You can buy greater Tokyo pass 5 day =7200 yen,cover narita airport haneda airport,odaw ara st by odakyu railway unlimited time 5days

While there is enough in Hakone to see that takes more than a day (there are a number of good places not widely publicized), I suggest that 3 days is too much. With that amount of time, you could see both the Hakone area as well as the Fuji 5 Lakes area, and a Fuji-Hakone Pass might suit you quite well. For Kamakura, you might consider adding in Enoshima, and there is an Odakyu pass for both.
Shirakawago is a nice place, but only takes a few hours. Don't miss the mountaintop overlook of the village.
https://youtu.be/lvtACNNuLUs

Six days in Kyoto is a good chunk of time to see the place. Just be sure to mix in some variety as well. If you just see an endless series of temples and shrines, it does get to be monotonous. There are enough places there to add some variety as well.
With 3 days in Hiroshima, you could branch out a bit too. There is Iwakuni, as well as Sandankyo Gorge, Kure, and the Senseki Garden in Higashihiroshima.
But I'd say one night in Koyasan is enough. There is little new that you'd get with a 2nd night there that you wouldn't just one night. Maybe if you want to go hiking a lot in the area though 2 nights might work - but you are already doing that later on. Otherwise, you can see all the main sights in 24 hours. If you want to see Okunoin at night, be sure to pick a temple with no evening curfew.
Osaka is really best at night - not as much interesting in the day that you won't see in Tokyo etc. You could take a day and go see Kobe. Osaka also has a few places you could keep as an alternate in case of bad weather, and for a trip like yours, it's nearly guaranteed to get hit with some rain on a given day.
https://goo.gl/K3RqXH

D26 - 28 Hiroshima - 3 days (daytrip to Miyajima Island) Hiroshima (3)
D29 Okayama Okayama (1)
D30 Himeji castle (no overnight) Osaka (1)

For D26-30, JR-West's Kansai Hiroshima Area Pass

https://www.westjr.co.jp/global/en/ticket/pass/kansai_hiroshima/

will suit you. If you purchase online (15800 yen), you can reserve seats online (from abroad). Normal one way ticket from Shin-Osaka to Hiroshima is 12000-13000 yen one way/person. Mizuho and Sakura train's reserved seats are somewhat more comfortable, so if they fit your plan, you may better use them.

Thanks to all of you for the insights and tips. :)

@ Ken: I have cut one night in Hakone and will stay in Kamakura instead as to be able to go back to Tokyo earlier if I have seen what I wanted. Adding Enoshima, it should, however, keep me busy for a little while... I kept two nights in Koyasan as I planned to hike there which would leave me no time to visit on the first day and I leave to Tanabe on the last day early in the morning. That makes for one full day to visit the place. All other recommendations seem very accurate and I will definitively include these in my planning. Thanks for the very detailed answer.

@ frog1954: The JR-West's Kansai Hiroshima Area Pass is indeed a good deal. Thanks for the advice.

I wish you all a very nice day! :)