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Help with Japan itinerary

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We are a mid-30s couple, traveling to Japan for the first time in May. We are looking for as well-rounded an experience as possible, given our brief trip. We have 13 days, 12 nights.

I'd love some feedback on the rough itinerary with a couple of caveats:
1) We prefer to stay no more than 3 places, and use these as home bases for exploring
2) We enjoy hiking/outdoor activities very much, however that is not our primary goal for this trip.
3) We haven't looked extensively into the train system yet, but are likely going to purchase the 14-day JR pass.
4) We don't want to be too tight on times/schedules as we don't speak Japanese and know we'll need to build in time for getting lost -- indeed, are looking forward to it!

All feedback is welcome, but particularly I'm curious whether we're missing sights we should see and whether the end portion of Takayama and environs is worth it on a limited trip. Other options to fill in the time would be Hiroshima/Miyajima or Fuji/Hakone area.

Arr. Tokyo Tuesday, 5/15/12 4:55 am:
5/15: Tokyo –
5/16: Tokyo –
5/17: Tokyo → Kamakura/Yokohama day trip
5/18: Tokyo – ?Kanda Matsuri festival
5/19: Tokyo → Nikko/Lake Chuzenji day trip
5/20: Tokyo → Kyoto
5/21: Kyoto – Temple market (Toji temple)
5/22: Kyoto → Nara
5/23: Kyoto
5/24: Kyoto
5/25: Kyoto → Kanazawa OR Takayama – Hida no Sato
5/26: Takayama/Nagano & Yudanaka Onsen vs. Shirakawa-go
5/27: Takayama → Tokyo

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