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How to split time between Tokyo and Kyoto with 9 full tourist days

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We will be going to Japan in mid-October, flying in and out of Haneda. Since we arrive late, our first night will be near JR Shinagawa station The next morning we plan on going to Kyoto by train. I already booked 3 nights there at Ryokan Shimizu . If we stay an additional night I'll probably book a regular hotel.

This arrangement gives us 3 days to tour Kyoto, and the remaining 6 for Tokyo (including a couple of day trips, and visiting with a friend living there). We can probably squeeze in an additional 1/2 day with the current schedule. Should we spend another day in Kyoto?

I was in Tokyo 25+ years ago for business, my husband has never been. I did some day trips at that time (Hakone, Nikko), but don't really remember much.

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