Your itinerary seems to be bit all over the place with a lot of back and forth.

I don't know where your interests lie, but unless you're completely uninterested in traditional Japan, you're not spending enough time in Kyoto, and geographically, running off to Hiroshima and Miyajima for a day and then coming back to Nara doesn't make sense. Kyoto and Nara are only half an hour apart by train.

You can also hit Hakone on the way back to Tokyo. Just be sure to take a Shinkansen that stops at Odawara (it will be a Kodama type), which is the gateway to Hakone.

I think that on the whole, you need a little more work with the maps and guidebooks.