3 week itinerary

Hello,

My dad and I are going to Japan in April and have the following itinerary:

Day 1 - Tokyo
Day 2 - Tokyo
Day 3 - Tokyo
Day 4 - Tokyo
Day 5 - Tokyo --> Kyoto
Day 6 - Kyoto
Day 7 - Kyoto
Day 8 - Kyoto --> Stop in Nara --> Osaka
Day 9 - Osaka
Day 10 - Osaka
Day 11 - Osaka --> Koyasan
Day 12 - Koyasan --> Himeji
Day 13 - Himeji --> Hiroshima
Day 14 - Hiroshima
Day 15 - Hiroshima --> Kobe
Day 16 - Kobe
Day 17 - Kobe --> Hakone
Day 18 - Hakone --> Nikko
Day 19 - Nikko --> Tokyo
Day 20 - Tokyo

At first I thought of getting a 21 day JR pass, but after some calculations I found out it would be cheaper to use some separate tickets and passes. For Tokyo - Kyoto we would buy a separate ticket and then use the Kansai wide pass for days 8 - 12, Setouchi pass for days 13 - 17 and Tokyo wide pass for days 18 - 20. However, I'm not sure whether this would be possible and I am mostly confused about what passes can be used to reach Hakone. Could you maybe help me to find out what the best pass(es) are to use for this itinerary?

Kind regards,

Winnie