I've only managed to get my hands on a JR pass once and have extremely little first hand experience of Japan outside of Tokyo.

I researched the possibility of saying in Himeji once, but the castle closes at around 5pm (6pm in the summer - last admissions one hour earlier) and opens at 10am, and with Kyoto, Hiroshima and Miyajima on the itinerary, it didn't seem worth doing.

Hopefully someone like railroadtycoon can confirm this, but my impression was that for journeys over 100kms long, stopovers were allowed, and for long journeys, those stopovers could be longer than a day
http://www.geocities.com/TheTropics/...50/ticket.html

So if I wanted to do this trip I'd look into leaving Tokyo very early (say at 7:33am) arriving at Himeji (in this case at 10:28am I don't see why arriving 2 hours later would make a big difference), touring the castle and continuing on to Hiroshima early that evening and staying there the first night. I'd just need to ensure that a stopover at Himeji was fine. I would assume that the easiest way to do this would be to reserve seats on the Tokyo-Himeji portion and seats on the later Himeji-Hiroshima portion at the same time I was booking the Tokyo-Hiroshima ticket.

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Apparently, stopovers might be a bit more complicated than I assumed - but still might be more or less doable if you're creative. I found this information
"Tips for Saving Money -- If your ticket is for travel covering more than 100km (62 miles), you can make as many stopovers en route as you wish as long as you complete your trip within the period of the ticket's validity. Tickets up to 200km (124 miles) are valid for 2 days, with 1 day added for each additional 200km. Note, too, that stopovers are granted only if your trip does not originate or end in Tokyo, Yokohama, Osaka, Nagoya, Kyoto, Kobe, Hiroshima, Kitakyushyu, Fukuoka, Sendai, or Sapporo. You can, however, purchase a ticket, say, in Takayama bound for Nagasaki (a total of about 1,860km/1,155 miles), stopping in Kyoto and Hiroshima along the way. In short, you can save money by purchasing tickets for long distances even though you plan to break up your journey."
http://www.sidestep.com/travel-info-...by_train_japan