Tokyo to Naoshima, Kyoto with JR Rail Pass

Hello!

I live in New York City, it will be my first time visiting Tokyo at the end May, with trips to Naoshima and Kyoto planned. I am a bit confused about what the best way would be to travel between these three areas.

I was wondering if it would be economically better for me to purchase a 7 day JR Rail Pass after I leave Tokyo?

This is my Itinerary so far:

• Stay in Tokyo for 7 days
• Leave Tokyo and go to Naoshima, using the JR Rail
• Leave Naoshima and go to Kyoto (what is the best way?)
• Leave Kyoto and go back to Tokyo (because we fly out of Narita airport)

Any help would be greatly appreciated.

Thank you so much!!!