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Japan Rail Pass vs Individual ticket purchase as needed

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Japan experts...please advise...

Need suggestions on whether we should buy the Japan Rail Pass for the following itinerary:

Day 1-We arrive in to Narita airport around 5pm.
Need transportation from Narita airport to Tokyo. Stay 1 night in Tokyo.

2)Take the Shinkansen to Kyoto. in Kyoto 4 nights.
Sight seeing around Kyoto by train, taxi, foot.

3) Take the Shinkansen back to Tokyo and spend 3 nights there.
Plan to tour Asakusa, Shibuya, Shinjuku, Ginza, Hakone, and maybe Kamakura.

4) Need Transportation back to Narita Airport

Questions I need help with...
1) what transportation should we used from/ to Narita airport to Tokyo?
2) By purchasing the Japan Rail pass, would it be the most economical and efficient way to tour Tokyo and Kyoto?
I read that the Japan Rail pass can be used on the Hikari Shinkansen ( Tokyo- Kyoto- Tokyo). This would save us from having to purchase additional tickets on the Shinkansen.

3) while touring Tokyo and Kyoto, would we be able to simply use the JRpass or would we need to purchase additional tickets? Can the JR pass be used on subways?

Any other advise, suggestions, and ideas for a fun and efficient way to get around Japan would be appreciated! Arigato minasan!

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