First time in Japan

Hi all,

we (four people) will be travelling in Japan in July for two weeks. We will be staying in Tokyo for a week and then we plan to head to the southern regions of Japan. Nikko, Hakone, Nagoya, Kyoto, Hiroshima, Osaka, Himeji Castle and to Naoshima island before returning back to Tokyo's airport. We are thinking of a day trip to Nikko while in Tokyo, one overnight stay (per place) in Hakone, Kyoto, and Hiroshima. From Hiroshima, we catch the train to Osaka where we stay for 3 days and explore the surrounding areas and finally we return back to Tokyo's airport. I would like to ask whether this itinerary makes any sense and is doable and for how many days we should book the JR pass? Are all those areas served with the JR pass or we need to get regional passes as well?

Thanks.