Our tentative itinerary is:
11/3 arriving Narita & staying in Tokyo Shinjuku
11/7 leaving Tokyo for Kyoto, staying in Kyoto..Maybe a side trip to Nara for a day trip while in Kyoto
11/11 returning to Tokyo Shinjuku from Kyoto
11/13 leaving Shinjuku for Narita airport
While we are in Tokyo, we might take a trip to Hakone or Nikko.
please advise..Thanks
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By going from Tokyo to Kansai round trip, plus using the Narita Express once back to the airport, you do make a 7 day pass pay off.
However, you have another option. You could use a japanican ticket.
http://www.japanican.com/en/tour/detail/VJOPENTK1/
You can save a lot more money this way, and even take the fastest bullet train, the Nozomi, to go there (you can't with the JR Pass). It does not cover the fares between the Kansai cities, nor to/from the airport, but you can still save more in the end.
Fares in Kansai aren't high, and you can use the 1000 yen bus for Narita.
http://accessnarita.jp/en/home/
So it's up to you.
To save money going to Nikko, get a Tobu Nikko Free Pass.
https://www.japan-guide.com/e/e2358_002.html
And for Hakone, get a Hakone Free Pass.
http://www.japan-guide.com/e/e2358_008.html
The Loop Course is a common way to see all the sights and takes a full day.
http://www.japan-guide.com/e/e5210.html
You can see regular fares, routes and schedules on Hyperdia.
http://www.hyperdia.com
Under "More Options", be sure to uncheck the Nozomi box since you can't ride that train if using the JR pass.
Hope that helps.