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Japan Rail Pass or individual train tickets or rental car?

We are a family of 5 (2 adults and 3 children ages 9, 12, and 14) traveling to Japan for 13 days from from June 15 - 28. I am uncertain whether it makes sense to purchase a JR Rail pass for our family given our itinerary. Can you please help advise us?

Arrive Tokyo Narita - Day 1 (June 15)
Tokyo - Day 1 - 5 (June 15 - 19)
Magome - Day 6 (June 20)
Takayama - (potentially with visit to Shirikawa) - Day 7-8 (June 21-22)
Kyoto - Days 9-13 (June 23-27)
Possible day trip to Nara
Back to Tokyo on Day 13 and leave from Haneda on Day 14 (June 28).

Will the JR Railpass work for our trips to Magome/Takayama/and Shirikawa? Or would it be better to rent a car for that leg of the trip and just do a pass for either the first week (while in Tokyo) or the second week (in Kyoto)? Or would it be more economical to purchase individual train tickets wherever we need them?

Thank you for whatever advice you can offer.


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