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11 days in Japan, JR pass question

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This October, my husband and I are stopping off Narita for 11 days on our way back to USA from Taipei. The whole trip is on AA and its oneworld partners.

This will be our 4th visit to Japan. Previously we visited Tokyo and Kyoto, and places in between them.

This time we'd like to visit Miyajima, Nagasaki, Kumamoto and Osaka using a JR pass, and minimizing our time in Tokyo.
If we were to purchase a 7-day JR pass, the schedule seemed a bit rush as below:

Day 1 - Train from NRT to Shinagawa. (Spend night in Shinagawa)
Day 2 - First day of JR Pass. Train from Shinagawa to Hiroshima. See Miyajima.
Day 3 - train from Hiroshima to Nagasaki.
Day 4 - Nagasaki
Day 5 - train from Nagasaki to Kumamoto. See castle.
Day 6 - train from Kumamoto to Osaka.
Day 7 - Osaka.
Day 8 - train from Osaka to Tokyo, because this is the 7th day of the rail pass.
Day 9 - Tokyo
Day10 - Tokyo
Day11 - fly off Narita at 6:45pm.

If we were to purchase a 14-day JR pass instead, it will allow us 2 more days to spread among our destinations before heading back to Tokyo on Day 10.

My question to you all is, can a JR pass be used to ride the Narita Express between NRT and Tokyo? How about using it to ride JR Metro line in Tokyo?

If it can be, then we could justify purchasing a 14-day rail pass and start using it on Day 1, utilizing it to the fullest, or as much as our time allows.

Thank you in advance.

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