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What is the most efficient order for this Japan itinerary?

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I will be flying into Narita and out of ITM. My itinerary covers:

4 or 5 nights Tokyo with possibly a day trip to Nikko ( ? using the Heritage Pass) or Kamakura
2 or 3 nights Kanazawa or a combination of Kanazawa and Takayama,
1 night Hiroshima, or Miajiima,
5 or 6 nights Kyoto.

Is there some way I can cover this itinerary using a 7 day JR pass. I am wondering what experienced Japan travellers think about this option: There is a bus that goes from Tokyo to Takayama in 3 hous and 10 minutes.. From there I could take a Nohi bus which stops in Shirakawa-go (this town is a definate on my itinerary) and continue on to Kanaazawa. I could then start the JR pass and go to Hiroshima and Miajiima, and continue on to Kyoto. Would I even need a JR pass for Kanazawa-Hiroshima-Miajiima Kyoto?

I haven't purchased plane tickets yet so could add on days if there is anything you would recommend seeing along the way. I was thinking of adding Matsumoto in the Japanese Alps. Would I be missing a lot if I skipped Hakone?

Thanks in advance for your help and for all the other helpful information I gained from reading the other Japan threads that are running at the moment.

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