This looks like a very very rushed schedule. My thoughts...

11/7 - Spend it in Kyoto. You're not doing it justice with only an evening spent there.
11/8 - Day trip to Nara or Kobe (definitely not both). Skip the Hiroshimo/Miyajima leg (which seems like a big detour for one day).

I recall someone mentioning that the JR pass is only worth it if you are doing Tokyo-Kyoto return. Since you're going one way, it might be worth it to calculate if it's really cheaper than buying individual tickets (especially if you choose not to do a day trip to Hiroshima). HyperDia will give you the exact costs. Remember with the JR pass you can't take the Nozomi, only the Hikari.

http://www.hyperdia.com/en/

Since you said this is not your one and only trip, you can always see the rest of the country on future trips. It's good to spend a little more time in the big cities.