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Japan Itinerary taking shape for October Trip

We were able to get non-stop roundtrip airfare Haneda/JFK with Frequent Flyer miles for mid October. Based on comments from my earlier post, here's my tentative itinerary:

Day 1 - arrive 10:15pm Haneda, head to hotel near Shinagawa station for the night (?Tokoyo Inn Sinagawaeki Takanawaguchi)
Day 2 –pick up 7 day JR Pass when station opens and head by train to Kyoto, tour kyoto
Day 3/4 - tour Kyoto
Day 5 – train back to Tokyo, tour Tokyo
Day 6/7/8/9 – tour Tokyo with day trips to Nikko (using JR Pass) and Hakone (have friend who will drive)
Day 10 – tour Tokyo, spend night at Haneda airport hotel (?Tokoyo Inn Haneda Kuko)
Day 11 – 6:40am flight home

I am looking at the Tokoyo Inns for the first and last nights for convenience's sake. Both stays will be quick overnights. We will look at nicer hotels for the Kyoto and Tokyo touring nights (around $200-250 range). Suggestions of hotels, and areas to stay are welcome for both cities. In Tokyo, convenience to transportation, with nearby restaurants are preferred, and not overly congested and touristy (like Times Sq).

I realize the Nikko day trip will be a long one, but I prefer not changing hotels more than I have to. We will aim for an early morning train, and return in the evening. I hope to visit some temples/shrines and also the Lake Chuzenji area. Maybe head to the lake area first thing when we arrive, then spend the rest of the day/evening touring temples.

I have a friend living in Tokyo who offered to take us to Hakone/Fuji, so no need to use JR Pass for that, but will do Nikko within the 7 day window of the pass.

I'd consider adding a day to Kyoto (taking from Tokyo) but with the day trips and spending time with my friend, I think that would make our Tokyo time too tight.

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