2nd trip to Japan (september/october) – Itinerary Ideas?

I’m travelling to Japan in September, arriving at Tokyo the 15th of September and leaving the 11th of October, so I have plenty of days. I’m looking for ideas to fill up the days, just general ideas on destinations and amount of days in each one, avoiding to repeat stuff I already visited as much as possible (my first trip was in February 2012 just for reference).

Places I already visited:

-Tokyo, though I’ll probably stay there for 6 or 7 days since there’s a lot I still didn’t see plus a couple side trips.

-Kamakura/Enoshima

-Nikko

-Takayama/Shirakawa-go (Might go again though because I went in winter and I imagine that it’s completely different in late summer/early fall)

-Kanazawa,

-Kyoto/Osaka (I might stay a couple days there though),

-Nara

-Hiroshima/Miyajima (I might go there again if it’s on the way to some place else because I really loved their okonomiyaki)

-Nagoya.

Places I definitely want to visit:

-Side trips to Mt Takao and Mt Mitake from Tokyo (so that’s already 2 days I’m staying in Tokyo covered)

-Some place near Mt Fuji, maybe Hakone, maybe Lake Kawaguchi, maybe both, how many days?

-Himeji, I think one day is enough for this one?

-Onomichi: I’m planning on staying 3 days there and doing the Shimanami Kaido on bike, with 1 day to visit the town, 1 day to cycle the route, and 1 extra day just in case.

Aside from that, I have nothing decided yet, I’ve been considering going to Kyushu or Shikoku, and then maybe flying all the way to Hokkaido and making my way back to Tokyo from there.

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