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Itinerary/tips for 2-3 weeks in Japan in Nov.

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Hi guys, I need some advice on an itinerary and whatever tips you have. I'm planning a trip this autumn from the mid-atlantic to Japan. Traveled extensively, never to east Asia, have been wanting to see Japan for a while. I hear the climate is quite similar to Washington DC, so November should be great for walking (fine with walking anywhere from 5 to 10 miles a day - although preferably not 10 a day every day), dry and cool. Would love to see some beautiful foliage.

About me:
-Young athletic man
-love to run and walk
-like art, music, archaeology, technology, some video/computer games, language, sports, love food/cooking, traditional arts, factory tours, books, bazaars/markets, produce, shopping, interesting shops, hiking.

I want to really get a good feel for Tokyo and therefore am thinking about spending 6-9 nights there. Don't want to be rushed, want to get a good mix of major sites that I also have an interest in (the crossing, asakusa, tsukiji market, akiba, daytrip to Nikko etc) but also whatever else seems interesting as I do my research (so far, odaiba island, a couple of museums, maybe a concert venue/concert, another daytrip baseball etc - would love your suggestions). However, since I also live so far away, I feel the need to see several different places in Japan in case I don't get a chance to go back soon. So I'm thinking 2-3 weeks for that reason (jetlag too). The best fares I'm finding are into Haneda and out of KIX, so that'll probably be my route (JR pass worth it?)

Things I absolutely want to do/see:
-Tsukiji market
-Odaiba island
-eat fantastic food (I know you don't have to break the bank to do this in Japan)
-hike for a day or two at least - intrigued by Kiso valley but the path looks a bit too short/easy (Tsumago-Magome)
-Stay at a ryokan/onsen
-spend some time in nature/mountains out of the city
-Kansai region (Osaka seems like an interesting city even if I only spend a night or two there)
-Tours of factories (sake, beer breweries) - whatever is interesting and available!
-See a Japanese castle (possibly Himeji)
-Spend time doing/see uniquely Japanese things (example: ryokan, sake brewery) that you can't do or see elsewhere
-At least one night in a capsule hotel

Things I am interested in, not as sure about:
-Alpen route/Tateyama mtns to hike and experience nature (in November, not going for the snow walls)
-Feel like I "should" see Kyoto and see more traditional architecture since I'll be very close
-Nara, perhaps a night there, perhaps a daytrip, thoughts?
-If not Tateyama, where else can I possibly spend a night or two between Tokyo and Kansai that I can be in a more rural/non-urban setting? Nagano prefecture seems to have a lot of beautiful places, any suggestions?
-Nagano itself. Worth my time? I do have a soft spot for less-touristed spots and minor cities where you can get a less hectic and more local feel while still having city amenities. Open to other suggestions as well.

I'm an experienced traveler (will be traveling alone, mostly in hostels), so I do enjoy spending more time in fewer areas instead of checking the boxes and moving on (ex: 2 nights Paris, rush to Eiffel Tower, Arc De Triomphe etc and then rush to 1 night in London to see everything...). I realize how much time and effort it takes to move from place to place, even by train and while in a different way I love train stations and airports, I don't want my trip to be spent mostly in them. I like having time to revisit areas I liked and mull around more residential or not as "on the map" areas even in big cities, but because of distance and financial/time restraints want to balance that with seeing more than just Tokyo/Kyoto. Can you please help me out with some possible itineraries and tips?

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