In that case, I'd just go early from Tokyo to Kyoto so you have 1-1/2 days for the city and 2 days for your day trips.

It is kind of a long haul down to Hiroshima so again, leave early if you want to have time for both Hiroshima AND Miyajima. The Rail Pass is good for the train from Hiroshima Station to Miyajima-guchi where you catch the ferry. It also covers one of the two ferry choices to Miyajima.

For such a short trip, the only thing you'll really have time to see in Hiroshima is the Peace Park. The tram from the Station to the nearest stop near the Park is 150 yen. Pay as you exit the tram. It will probably be easier to go directly from Hiroshima Station to Miyajima-guchi as soon as you arrive and save the Peace Park for the afternoon when you return but again YMMV.

The Tourist Information Center just outside Hiroshima Station has some pretty good maps in English but basically, you'll just take tram #1 and get off at the Fukuro-machi stop, walk another half-block in the same direction to the huge NHK building, turn right and walk across the bridge to the Peace Park. Return the same way but catch the same tram on the other side of the street going back to the station.

If you want to take that extra day you are playing with and add it to Kyoto, you could also take a day trip to Hikone on Lake Biwa to see an original feudal-era castle. The castle in Hiroshima is a reproduction and the famous castle at Himeji is currently covered in construction tarps. You can't even see the castle from the train as you go by any more.