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Japan Itinerary for 12 Nights and 13 Days

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Hello All,

My husband and I will be travelling to Japan for the first time this October/November for 13 days and 12 Nights. We are a couple in our early 30s and this is a much needed break for the both of us.I know its a little too late but this was a last minute decision. We like to be on budget with occasional relaxation.We love culture, history and we would probably make it in time for the autumn foliage. We will be flying into NRT on Oct 27 and depart from NRT on 8th November.
I have been keenly following the previous posts on the various itineraries, yet I remain confused on how to plan one for Japan. Based on the itineraries from other posts and also with a little help from japan-guide I came up with the following itinerary.

Please guide me with the following queries:
1. Are we spending too much time in Tokyo ? If yes, how can we adjust the plan ?
2. We intend to take the 7 day JR Pass. But from the looks of the plan, I would need a 14 day plan. Which doesn't seem efficient considering we will be using the 14 day plan for 8 days only. Do you see a way we can make the most of 7 day or the 14 day with the itinerary below ?
3. We wanted to include Takayama in the plan. However, adding Takayama looks like we will be super packed. Any suggestions if I would need to re-arrange this plan ?

27-10-2017 - (Day1) - Arrive in NRT and reach Tokyo by early evening.
28-10-2017 - (Day2) - Tokyo
29-10-2017 - (Day3) - Tokyo
30-10-2017 - (Day4) - Tokyo
31-10-2017 - (Day5) - Shinjuku to Hakone - Use Hakone Free Pass - Stay the night in Hakone
01-11-2017 - (Day6) - Hakone - Kyoto
02-11-2017 - (Day7) - Kyoto
03-11-2017 - (Day8) - Kyoto
04-11-2017 - (Day9) - Kyoto
05-11-2017 - (Day10) - Kyoto - Nara (Day trip)
06-11-2017 - (Day11) - Kyoto to Hiroshima. Stay at Miyajima
07-11-2017 - (Day12) - Tokyo
08-11-2017 - (Day13) - Tokyo - Flight in the evening. Return.

I appreciate your time and your suggestions are welcome.
Thank you very much !

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