Hello. I spent 3 weeks in Japan in 07 and went to many places with the rail pass. But even my itinerary wasn't this packed. It needs to be cut down quite a bit. But doing that will make your trip much better.
As for Takayama or Kanazawa, I did not go to either, but looking at this site, I'd recommend Kanazawa because of the Kenrouken garden. Takayama has a historic district, but it looks like Kanazawa does too.
Day 1-6 can remain the same with adding a night stay in Koyosan. As for Day 7 of your trip, I'd travel from Kyoto, stop in Himeji. See the castle for a couple hours in the morning, and then keep going to Hiroshima in time to go to the museum there and see the Peace Park. Then for Day 8, go to Miyajima island. Make sure to climb to the top of Mt. Misen and if it's cloudy, it can clear up in the afternoon for an awesome view (it did that for me). Then Day 9 leave Hiroshima and go to Kanazawa via Osaka. This would leave you just the afternoon to view the garden. Day 10 travel to Shirakawago and then spend the night there. Day 11, 12, 13, 14, and 15 I'd stay in Tokyo. I did not go to Hakone, but I did go to Fuji Five Lakes. If you want to go to Hakone primarily to see Mt. Fuji, I would instead go to Fuji Five Lakes, by taking the Express train from Shinjuku (in Tokyo) and then transferring at Otsuki to the train that takes you to Kawaguchiko (Fuji Five Lakes area). It's right next to the mountain, as opposed to Hakone. You can tour the area, hike near the base near the Ice Cave and Wind Cave (go in those two, and in the Bat Cave, very fun), and view the whole area and Mt. Fuji from a hill that you get to by ropeway. When I went to see Mt. Fuji, I wanted to make sure that the skies were clear, so during my stay in Tokyo, I checked the weather forecast daily, and when it was forecast to be clear, I left on that day for Fuji Five Lakes. I was rewarded by an excellent view of Mt. Fuji the whole day. Being flexible is the key. As for Kamakura, I did not go here, but I've read that if you go to Nara and see the big Buddha statue (which I did) and see the many temples in Kyoto (which I did), Kamakura is not necessary. I would recommend cutting out Kamakura. But for Nikko, I would recommend going there as a day trip from Tokyo. Very beautiful shrines and a beautiful forested area.
So basically, if you're in Tokyo for 5 days, two of those days could be for Nikko and either Fuji Five Lakes or Hakone. And then 3 full days in Tokyo. I would recommend at least those 3 days (not just 2) because Tokyo is so gigantic and there are so many fun and great places to explore there.
The tightest part of this itinerary would be traveling from Hiroshima to Kanazawa. Hopefully this would work, but you might want to look into it some more.
Good luck and I hope this helps. Have fun!!!
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