Resist the temptation to feel like you need to "see it all." You can always go back(In fact, I bet you will ;-) ). My best travel experiences have been when I spend at least 3-4 good days in a city like Kyoto(or Tokyo). It gives you time to get your bearings and really appreciate what you are seeing.

Hiroshima/Miyajima day trips from Kyoto will feel hectic, to say the least. You might get away with just Hiroshima from Kyoto for a day.

My suggestion would be to drop the Hakone day trip from your Tokyo itin. To be honest I didn't find it that enjoyable.
A rough outline could look something like this:

arrive
Tokyo x 2 days
kyoto x 4 days(1 day for nara)
hiroshima/miyajima x 2 days
tokyo x 3 days
go home

This way you aren't having to go back and forth over long distances for day trips. My personal experience is that its always great to end the trip back in Tokyo.

Just my opinion. It takes a little time to get out to Miyajima. Consider spending a night on the island!