We will be 13 full days in Japan - 6 nights in Tokyo, 2 nights in Naoshima, 5 nights in Kyoto.
Arriving to Tokyo, then to Naoshima, then to Kyoto and from Kyoto straight to Narita (or flight is around 17:00).
We are planning to get 14 day JR pass. Would it cover each of these legs of the itinerary? (I know, for example, that ferry to Naoshima is not covered).
What about the final leg - from Kyoto to Narita? Do we have to make seat reservation in advance? Do we need to make train changes?
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You have two choices - use a 7 day pass and shorten your time in Kyoto, or get the 14 day pass and add a side trip or two from Tokyo to somewhere like Nikko, Karuizawa, Izu, Kusatsu, etc. I favor the latter - 3 or 4 days in Tokyo are quite enough, and there are many good places nearby to visit.
The JR Pass would cover all legs that you mention. Yes, seat reservations for the Narita Express are required, and you can do it at any JR office or just before you board your train to Narita, either Shinagawa or Tokyo Stn.
It requires at least one transfer.
There quite a few possibilities to reach Narita by rail, both JR and not.