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JR Pass use Information in Kyoto, Nara and Tokyo

Hello, I live in Italy, I booked a trip to Japan from November 21 to November 28, and there are two pairs, in Narita airport arrival and the first three days in a hotel in Nara and then return to Tokyo (Shinjuku Hotel ), I wanted to know if from Narita to Kyoto (or Nara) there is a direct JR train (going to book my JR pass) and if from Nara to Kyoto by JR Line also stops at Fushimi Inari Shrine and if appropriate to take one of PASMO or Suica card for use in Kyoto subway or bus to travel in town and travel to Tokyo for a metro and bus.
Thanks and sorry for my bad English
tiziano58

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    If you travel from Narita down to Kansai (Kyoto/Nara/Osaka/Kobe) and return to Tokyo within 7 days, then a 7 day JR Rail Pass would pay off. There is no direct train though - you can take the Narita Express train from the airport to Tokyo station, and then ride the bullet train to Kyoto. The Narita Express takes almost an hour, and from Tokyo to Kyoto takes about 3 hours.

    Yes, the Nara rail line from Kyoto Station stops at Inari Station (only 2 stops from Kyoto Station), and the Fushimi Inari Shrine is just across the street. It is free and open 24/7, so if you go there in the early morning or evening, you can avoid a lot of the crowds. You can use the Pasmo or Suica cards, but if you spend the whole day in Kyoto, there is a 500 yen bus day pass that can save you a lot. Nara has one too, but most of the best sights are in Nara Park, and you can walk there 20 minutes from the JR Nara Station.
    Since you are already seeing Tokyo, you can largely skip Osaka during the day. After the temples of Kyoto close down around 5PM, you can go over to Osaka for the evening. At night the city comes alive and has some great places to see, such as Dotonbori, plus the night views from the Umeda Sky Bldg and Abeno Harukas Bldg are wonderful. On another evening, if you have the energy you can also go see Kobe. And if you have time, taking a day to see Himeji with Japan's finest castle is well worth it too.

    If you are spending a few days in Tokyo, then a 2 or 3 day subway day pass can save you a lot of money also.
    http://www.tokyometro.jp/en/ticket/value/travel/index.html#anc03
    The Pasmo or Suica cards don't give you any discounts, they are just convenient to not have to carry around heavy coins everywhere.

    You will be in Japan in autumn leaf season, called 'koyo'. It is one of the most beautiful times to visit Japan, but places in Kyoto will be more crowded. You should see it though - it is unforgettable. Here are some famous spots:
    http://www.japan-guide.com/e/e2014_where.html
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    Thanks TENJIN the answer I forgot to ask for a piece of information, when they are in Tokyo Hotel in Shinjuku one day I wanted to go visit Omiya (The Omiya Bonsai Art Museum) I'm a bonsai artist and wanted to ask if you can take a JR Line from Shinjuku using the JR Pass, or should I use another private line?
    Thank you
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    You can easily get there by JR, with one transfer along the way.
    Have a look for example at:
    http://bit.ly/29Arbi7
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