Hi there, we are planning a trip to Japan, and I need some advice regarding the JR Pass, we fly into Narita at 19:00 and make our way to Shinjuku for 3 nights from there we travel to Hakone for 3 nights, then Kyoto for 4 nights, Hiroshima for 1 night, Osaka for 2 nights, then back to Narita. Will a pass be valid for these places? Thanks in advance
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With the exception of the Mt. Fuji area, you can use the pass to all the places and since you plan to go down as far as Hiroshima, a 14 day pass will pay off.
I would say though that 3 nights in Hakone are way too much. You could cut back a day, and use it to see Nikko, which is one of the best places in Japan. To get to Hakone, you can take the bullet train down to Odawara, and then I suggest you get one of the Odakyu passes. If you're spending that much time in the area, you might also go to see the Fuji 5 Lakes area as well.
http://www.odakyu.jp/english/deels/
For Kyoto, keep at least half a day to see Nara as well. It has some of the best places you'll see in Japan.
http://www.japan-guide.com/e/e2165.html
Since you are already seeing Tokyo, you can largely skip Osaka during the day. After the temples of Kyoto close down around 5PM, you can zip over to Osaka for the evening. At night the city comes alive and has some great places to see, such as Dotonbori, plus the night views from the Umeda Sky Bldg and Abeno Harukas Bldg are wonderful.
Instead, you might take a day to see Himeji, with Japan's finest castle, Kokoen Garden next door, and on the way back Kobe has some very nice sights.
For Hiroshima, don't skip Miyajima either, and if you still have time, Iwakuni is just a bit beyond it and has some iconic sights.
There are some good previews of the places you plan to see on:
https://www.youtube.com/user/thejapanfaq/videos
Yes the Narita Express is covered. All JR routes are covered, but if you take a non-JR line near Kyoto such as Kintetsu or Hankyu, they are not covered.
For Hiroshima City though, the JR Pass does cover the Loop Bus.