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How many nights in Tokyo/Kyoto/Osaka? Organizing an itinerary?

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All right. So I've been doing a lot of research on Japan Guide and I've got several guide books. I still don't have a good grasp on how much time I need in the major cities. I thought I'd ask here because Fodorites tend to be fans of slow travel.

Day trips (Or overnight?): naoshima (actually, setouchi trienale as a whole), Nikko.
Activities: Disneysea, the fabric district, tokyo national museum, the Imperial palace area, studio ghibli, shopping in daikanyama, kagurazaka, national Showa museum, koishikawa korakuen

Kyoto: so many shrines and temples I don't even know where to start. But certainly the fushimi Inari shrine and the otagi Nenbutsu-ji . Would 7 nights be too much? Too little? Nara (day or overnight? Multiple nights?)

Mount Koya- not sure if this is more accessible from Kyoto or Osaka.

Hiroshima: the memorial, miyajima island (day or overnight trip?) anything else?

I'd like to do the walk between Magome and tsumago. Can't figure out where to put that though because I haven't decided what order to put the cities in. I understand that it's part of the "Japanese romantics road" so perhaps I should add a day or two to enjoy the area?

Also interested in hakone and the alpine route. Is one superior to the other? Both worth visiting for their unique aspects?

Then also Takayama and and Kanazawa look worthy of a few nights. thoughts on either?

As a Ghibli geek, I'm also also interested in visiting dogo onsen in matsuyama, and yakushima island. I'm thinking that matsuyama is easier to reach but Yakushima is more along the lines of my interests.

I was going to ask about booking a temple for an overnight stay. But I cannot figure out where I had in mind. Perhaps it was mount koya? Has anyone done this? Did you enjoy the experience?

Mostly I plan to stay in hostels, and I plan to buy a JR pass but I cannot decide which one would be best.

My two possible starting points are Osaka and Tokyo. Osaka is looking much cheaper to fly in and out of. But I usually fly open jaw, and I am not sure if I'd find a round trip ticket a hassle.

So Osaka would probably eat at least one night. Any thing you really enjoyed there?

I love museums, history, nature, food. Textiles, daily life, art, mostly, although I'll go to an excellent war or technology museum. Unesco sites are of particular interest. I like all sizes of towns or cities and I'd like to mix it up a bit. So I want to stay long enough in the cities to get a good feel for the place, but I don't want the cities to take up the lions share of the trip. If that makes sense? I hope it does.

Any other places you absolutely loved, please do fell free to add!

Also interested in excursions such as bike tours or kayaking, if anyone has done something like that they'd recommend.

Thank you for any feedback!

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