& day JR pass plus itinerary...worth it?

A 7 day pass would pay off, used during the last 7 days of you trip.
If you are arriving at Narita when you enter Japan, you can get into Tokyo cheaply with a [Keisei/Metro] package, or use a 1000 yen bus with a 3 day subway pass.
The JR Pass will not take you all the way to Hakone, however. You should look into getting a Hakone Free Pass. Kobe is a nice city with some good sights - but you could also fit in seeing Himeji Castle, which is Japan's finest. The JR Pass will not help you much in Kyoto either - look into getting a 500 yen bus day pass. Be sure to take half a day and see Nara as well. The Todaiji Great Buddha is a must-see place and in Nara Park there are many others as well, including Kasuga Shrine, Kofukuji Temple, feeding the deer, plus the Yoshikien and Isuien Gardens.
If you want to see Hiroshima and Miyajima in a day, then start early and cover the main sights (Peace Park/Museum, castle, and Shukkeien Garden) and then put the majority of your time into seeing Miyajima. Be sure to take a stroll around there in the evening as well - once the tourist crowds leave by sunset, it gets very quiet and peaceful.

thanks so much, very useful and informative!