Frommer's guides usually have entries on travelling with children and always list "family-friendly" hotel choices.
I agree with
jpatokal that Hiroshima is a long haul unless you are spending a night or two. If so, definitely plan on a half-day at Miyajima. It is a post card waiting to happen.
Some info:
The JR express train from NRT to Tokyo is a little over an hour. Much cheaper (and nicer) is the Keisei Skyliner which takes 1 1/4 hour and arrives at Ueno station rather than Tokyo main station. Depending on where you are staying, the Skyliner may be a better bet. From either station, you will probably have to cab the last little bit to your hotel. There is also a limo bus option which will take you right to some up-scale hotels or to the main train station. DO NOT TAKE A CAB to/from NRT - it will run almost $300.00.
The shinkansen from Tokyo to Kyoto will take about 2 1/2 hours for the Hikari trains available to JR pass holders. The Nozomi is faster but you can't use the pass on the Nozomi. There are far fewer Hikaris than Nozomis, so check the schedule at eki-net and plan accordingly.
The shinkansen from Kyoto to Himeji is less than an hour. The JR train from Kyoto to Nara (an excellent daytrip) is around an hour.
The JR Haruka deluxe train from Kyoto to KIX is 1 1/4 hour.
If you will be spending a few days in and around Tokyo, the subways are the best travel option. The best $10.00 you will spend in advance would be for Kodansha's Pocket Tokyo Subway Guide from Amazon.com. "Don't leave home without it."
For a semi-Japanese ryokan experience on a budget, I can highly recommend the Ryokan Asakusa Shigetsu in Asakusa, Tokyo. Located in an older section of Tokyo outside the hustle-bustle of the central city, it is very near two subway lines, Senso-ji temple and the Nakamise outdoor shopping arcade. I usually take the Skyliner from NRT to Ueno then catch a cab to Asakusa for less than 2000y. The subway is noprmally cheaper and more convenient but not with luggage.
www.shigetsu.com
The only problem might be finding it in a cab, but the website has a map that can be printed out.
There are lots of other "reasonable" accommodations out there via the 'net.
JR