I think you have a pretty good general itin. If your flight isn't booked, I would consider flying into NRT and out of KIX or ITM so you don't have to backtrack to Tokyo on your way out.

I would think about spending one less day in Tokyo, and then using your railpass to go to Nara and/or Himeji, staying based in Kyoto. Lots of people want to visit Hiroshima, but I think the peace museum is overrated (Nagasaki's is much better). However, Miyajima (just outside of Hiroshima) is worth it.

I think it comes down to the types of things you want to see, and how much you want to be traveling. For history/historical architecture, Kyoto/Nara/Nikko/Himeji. For natural beauty, Miyajima. For modern Japan, Tokyo and Osaka. Of course these are generalizations, but you get the idea.

Nara can be done in a day from Kyoto, and Himeji can be done in less.

Of course, you could have plenty to do in Tokyo alone for a week, but I think you need to leave Tokyo to get a broader sense of "Japan," especially if you don't plan to return.