Do you do all booking online?
I didn't feel comfortable doing that, so I called our Kyoto Ryokan and spoke to a lovely woman who held my reservation until I can mail her the deposit check. The price was the same (or less) than those advertised online. I guess maybe hotels are a different story.
What is a good web site to find deals on Hiroshima hotels?
(We used points to get our Tokyo hotel.)
How far ahead do I need to get the JR pass?

Personaly I do no hotel bookings on line. Happy Travels!

Yes and I am quite comfortable doing it. I have also called Japan to book lodging. Have never sent a deposit but have given my cc number to hold the reservation. Sometimes the cancellation policy requires 24 or maybe 72 hours advance. Have never had a problem with having a reservation honored or having one cancelled.

For hotels, a good way to make reservations online is on their Japanese web page.

You could try jtbusa.com or jalpak.com

You need to get a voucher for a JR Pass before you get on the plane to go to Japan.
http://www.japanrailpass.net/eng/en001.html

Your son, the student in Japan, may not be eligible for a JR Pass.

Thanks for the input.
I guess it's what you feel comfortable with. I will probably call. A couple of extra bucks for peace of mind is worth it to me.
My son has student rail passes(really cheap!). I think he can travel on most trains, so hopefully no problem. He will have been traveling on those for 3 weeks by the time we meet up so I'm counting on him to have that worked out (I know, not a good plan to count on a 20 year old guy).
mrwunrfl - thank you for all of you helpful replys to this and my other posts. So many questions, so little time!

With student rail passes, you have to be really careful how you use them...as far as I know, they are only good on local trains, and if you ride others, you need to pay a hefty supplement. They are also seasonal, valid only at certain times of year...that part is easy to figure out though. Which trains you can ride is more challenging. He should really carefully check this before purchasing one, and you as well...since if he can only ride locals, you'll either want to ride locals with him (in which case you do not need a JR pass as the local train price is so cheap - hence the student pass cheap) or you'll need to pay lots extra for him to ride with you on the good trains. Really, check carefully about his pass before deciding on buying his and yours.

That's good advice to check the pass terms closely. Does anyone know where those student passes are described? I hadn't heard of them before.

If you were to take JR local trains (at least two changes of train) it would take 6 to 7 hours to travel between Hiroshima and Kyoto. With a regular JR Pass, using the shinkansen, it would take less than 2 hours (with one change).

The base fare from Hiroshima and Kyoto, shown at hyperdia, is 6300 yen. You would pay that for the local trains. Hyperdia shows that fare for the shinkansen but adds on a charge of 4490. That is a 3790 surcharge plus 700 for a reserved seat. Those are one-way prices. Your JR Pass would cover all of that but the student pass would almost certainly require payment for the surcharge and reserved seat charge, and maybe part of the fare (if not all of it).

The student passes are for Japan residents, though anyone can buy them. I've seen them publicized on the university bulletin boards as well as at the station. There are also passes for those over 60, for those travelling within a certain time period...JR offers lots of discount plans for just about every population, but they have so many restrictions as to when and how you can travel most people never give them a second thought. They are great for those with unlimited time for travelling and the ability to travel within the date restrictions, though.