Itinerary check for 13 days: (Tokyo, Kawaguchiko, Kyoto, Amanohashidate, Osaka, Hiroshima)

Hi, need some help with planning my first Japan trip! I’m unsure if some of these things are doable as day trips or not but I think they’re manageable.

I’m planning on buying a Jr Pass and activating it on the day we leave for Kyoto. It won’t cover the day we return unfortunately but from what I’ve calculated, it should cover everything else and especially if I plan on seeing the Kawaguchiko, Hiroshima, Miyajima, and Amanohashidatte. Please correct me if I’m wrong.

I’m also a bit unsure about the IC cards. Does the IC card (any one of them) cover all of the city trains I’ll be taking in Tokyo and will they also work in the other cities? What confuses me is when I read something like “Suica is the prepaid IC card by JR East for JR trains” because, from my understanding, all trains are not JR trains.

Here’s the itinerary in a not-so-detailed form, especially Tokyo where I will just try to do whatever I feel like:

EDIT: I’ll be in Japan from the end of august until just before mid September

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* Day 1 Tokyo: Shibuya and Harujuku.
* Day 2 Tokyo: Sensoji Temple Asakusa in the morning followed by Akihabara.
* Day 3 Yokohama? Is Yokohama worth a day trip?
* Day 4 Tokyo: • Ikebukuro Sunshine City • Shinjuku
* Day 5 Tokyo to Kyoto train I want to see Lake Kawaguchiko on my way to Kyoto. Don’t plan on doing anything of significance in Kyoto on this day so it might as well take up the whole day. Any tips on how this is achievable?
* Day 6 Kyoto: Historic Kyoto

Fushimi Inari quick visit (maybe) before going to Kiyomizu. • Kiyomizu-dera and the street
leading up to it • Afterwards walk downhill toward Yasaka Pagoda Gion Street is right across,
Yasaka Jinja is also located here. • 5 min walk to Hanamikoji street, famous geisha district. •
Next to the backstreets of Kyoto, Pontocho

* Day 7 Kyoto: Nature

The Keifuku Randen Tram Line to Arashiyama. • Arashiyama for the bamboo grove and walk
around. • Sagano Railway, 25-minute train ride, JR train to return or a 2-hour river cruise. • Come
back out to the waterfall and river at the Togetsukyo bridge. • Head up to the Iwatayama
monkey park? • End the day with Kinkaku Ji, if I have the energy Day

* Day 10: Amanohashidate Day trip to if we can manage? Ine near Amanohashidate. Return to Kyoto by 6 pm.
* Day 9 Osaka: • Shitenoji Temple • Then a short walk to Shinsekai. • Harukas 300 • Dotonbori
* Day 10 Osaka: • Osaka castle • Head to Dotonbori again. • Shinsaibashi or Ebisubashi for shopping, arcades. • Amerikamura?
* Day 11 Hiroshima and Miyajima? Daytrip • Train to Hiroshima and then the ferry to Miyajima. Spend a couple of hours on the island before heading back to Hiroshima for a few more hours. Back to Osaka to the hotel.
* Day 12 Nara and Train back to Tokyo
* Day 13 Tokyo. • Have a lot of hours to spend in Tokyo before the flight.

Thanks in advance