Hi - we arrive in Tokyo on 7th October, where we will spend a few days. We will then go to Kyoto for 3 days, then Nagasaki for 3 days then back to Tokyo. Is the 14 day rail pass the best one to get, and do you have any views on our rough itinerary please
14 days in Japan flexible

Hi there,
I would use a 7 day Japan Rail Pass, if you can cover the trip to Kyoto, Nagasaki and back to Tokyo with it. That said, a 14 day JR Pass would work well too, as you do enough travel to make savings with either pass.
Also note that doing Nagasaki - Tokyo in one go is quite a long trip. It might be nice to add a stop-over in between. Places I'd recommend would be Himeji or Nagoya.
Kind regards,
Daniel
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