Hiroshima and Himeji are in the opposite direction from Kyoto as compared to Tokyo. No, you can't visit sites at either of those on the same day as going to Tokyo. I suggest looking at this web site, which has very good information about things to see and also maps so you can understand where things are.
There are people who day trip Hiroshima/Miyajima from Osaka/Kyoto, but you cannot visit Hiroshima and Himeji and go to Tokyo, which is in the opposite direction from Kyoto/Osaka. I recommend you to stay at Hiroshima for 1 night, if you cannot stay at Miyajima: you can find more inexpensive hotels there.
For a midweek day in September, I see some good rates at https://www.booking.com for hotels near Hiroshima Station, including US99 (about 11,000 yen) at the very nice Granvia, right next to the station: http://www.booking.com/Share-1k3QN4 I saw other cheaper hotels but am not familiar with them. Miyajimaguchi (where you catch the ferry) is a half hour from Hirsoshima Station, with a train about every 15 minutes.