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15 Days in Japan, Itinerary Help Please

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I am going to Japan in mid to late September for 15 days. I spent four days in Tokyo about 15 years ago, and I did not love it (loved the Park Hyatt, but not the location...Had bad jet lag which greatly affected the trip, though it made it easy to go to Tsukiji, which was great). I've been to Kyoto twice, and I love it; it is one of my favorite places. I want to give Tokyo another chance. I am traveling alone, and I normally travel to cities, not beaches or or more rural, quiet places (but I am open to this). I like architecture, great food, photography (I am a serious photographer),nightlife, walking (exploring neighborhoods), culture and history.

I am somewhat constrained by my current hotel reservations in Kyoto (three nights) and Tokyo (six nights, plan on day trips to Kamakura and possibly Nikko), which were based on my originally planned shorter trip. I would like to keep these reservations as they are. I would consider another night or two in Kyoto, if it makes sense. So, essentially, I have about five days before I go to Kyoto for which to plan an itinerary. I assume I should get a rail pass and explore the country; possible places to go to (?): Hakone....the Alps...Kanazawa...Nikko...a night in a ryokan... Onsen...A night in a temple at Koyasan ...Hiroshima...Kobe. I would appreciate help and guidance, and the smartest logistics and routing.

My current itinerary:
Day 1: Arrive Narita 5:00 pm, Overnight in Tokyo.
Day 2:Tokyo-?
Day 3: ?
Day 4: ?
Day 5: ?
Day 6: ? (Add a day to Kyoto?)
Day 7: ?-Kyoto
Day 8:Kyoto
Day 9:Kyoto
Day 10:Kyoto-Tokyo
Day 11:Tokyo
Day 12:Tokyo
Day 13:Tokyo
Day 14:Tokyo
Day 15:Tokyo
Day 16: Depart Tokyo

I am assuming all travel will be by train (hopefully Shinkansen, though I understand there are some limitations with a rail pass?).

Thank you for the help.

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