Hello. I would suggest definitely buying the 7 day JR pass, and using it to do the following (I did a similar thing when I was in Japan and I really enjoyed it): 1st day: travel to Kansai region. (I'd stay next to Shin Osaka station, b/c then you can go to both Osaka and Kyoto easily (Kyoto quickly by jumping on shinkansen with JR pass), and it's cheaper than staying in Kyoto.) Visit Osaka or Kyoto after arriving.
2nd, 3rd, and 4th day visit Kyoto, Osaka, and Nara (whichever places intrigue you the most, all within fairly close distance). When I went to Japan in 2007, I liked Osaka Castle, Osaka aquarium, Nara, Fushimi Inari Temple (can go to on same day as trip to Nara), Kiyomizudera Temple, and Arashiyama (esp. climbing up hill at the monkey park and seeing view of Kyoto).
5th day: Take shinkansen to Himeji. See Himeji castle. Then continue to Hiroshima in the afternoon. Visit places in Hiroshima that evening. Try the famous okonomiyaki for dinner. Also the oysters in this area are great too.
6th day: Take train to Miyajima, take ferry to the island. Very beautiful, hopefully will be clear weather, at least for part of the day, b/c of great views from top of Mt. Misen.
7th day: Visit Peace Park and Peace Memorial Museum, and possibly other site in Hiroshima. Make sure to leave by around 4 or 5pm b/c shinkansen back to Tokyo will take about 4 to 5 hours.
For the 7 days when you can't use the rail pass, I would suggest spending at least 3 full days in Tokyo. You could base yourself in Tokyo this week and take a few day trips. If you did this, you could wait and see if the weather will be clear for a day at Mt. Fuji, and leave fairly early in the morning by train and go to Fuji Five Lakes, if you are interested in seeing Mt. Fuji. There are neat caves to go in around there too. There is also Kamakura, Yokohama, and Nikko to visit. If you go to Nikko, you might want to stay a night or two near Nikko, or you could make it a long day trip. But there are many many things you could do near Tokyo, in addition to thing to do in Tokyo. I would read up. Buy Frommer's Japan, Lonely Planet Japan, Day Walks Near Tokyo (avail. online used), TimeOut Tokyo, definitely buy Tokyo City Atlas: A Bilingual Guide, and Streetwise Tokyo Map. Japan Atlas: A Bilingual Guide is also useful.
Hope this helps. Have fun planning!
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