Hi,
For your time schedule, none of the passes would work. But with a few small additions, a 7 day pass would pay off for days 1-7 if you added at least half a day for a trip to HImeji, which has Japan's finest castle, or some other fairly distant alternative. Osaka has some sights of course but is better at night for great places like Dotonbori, plus the night views from the Umeda Sky Bldg, and Abeno Harukas Bldg. After the temples of Kyoto close down around 5PM, you can zip over to Osaka for the evening. Also take at least half a day and go see Nara - the Todaiji Great Buddha is a muse-see place and there are other great places in Nara Park there as well, including Kasuga Shrine, Kofukuji Temple, Yoshikien and Isuien Garden.
That would get you into Kamikochi, and from there you can use a 3 day Kanto Area Pass to get back to Tokyo, see Nikko, as well as Shimoda. You can buy it at Narita Airport and designate your first day as Day 8. To be honest though you can't actually take JR into Kamikochi - you can only go so far as Matsumoto - from there you must pay for a non-JR Matsumoto Electric Railway up to Shin-Shimashima Station (30 minutes), and then pay for a bus to Kamikochi (one hour). The JR Pass doesn't cover that.
For getting back to Narita, look into a 1000 yen bus.