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Early stages of planning trip to Japan (Tokyo and Kyoto)

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I just got a good deal with my frequent flyer miles for round-trip airfare to Tokyo Haneda from JFK in October. We will be arriving late on a Thursday night (around 10:15pm). We will have 10 nights in Tokyo (9 touring days). I'd like to split my time between Tokyo and Kyoto with maybe a day trip or 2 from Tokyo.

My thought is to spend our first night at a hotel very near Shinagawa Station. I am anticipating this first night will not be all that restful from the time difference. The next morning, we'd have breakfast and then catch a train to Kyoto. I'm figuring we'll get some additional sleep on the train. We'd try to catch something around 9ish so we are in Kyoto by noon (I understand trip is about 2.5 hrs).

We would then spend 3 nights in Kyoto, and return to Tokyo for the last 6 nights. Our return flight is very early, 6:40am.

1. Does this general itinerary make sense?
2. How do we most easily get from Haneda to a hotel near Shinagawa at around 11pm-ish, and about what would be the cost (need to get some yen in advance to be safe)? In this situation, we are looking for the quickest/easiest solution.
3. What area of Tokyo should we stay? Prefer not a times square-like overly touristy area, but near public transportation and some decent "local" restaurants and charm. We would like to keep hotel under $200 but anything up to $250 would be considered.
4. Should we spend the last night close to the airport? If not, what's the best transportation option to the airport, how much time and approx. cost (I guess this depends on where in Tokyo we stay)?

I was in Tokyo twice before for business, but that was 25+ years ago. My husband has never been. I've heard Kyoto is beautiful, and in the fall we may get some nice foliage.

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