I think most things have already been said. Travelling by rail in Japan is very easy, even if you don't speak the language, but as long as you can speak English. I read somewhere that before the football (soccer) world cup in 2002 they changed all of the signs in stations to be multilingual, and I found that to be true even in some very remote places, they were all in Kanji, Hiragana and English. Even local services have signs and announcements in English.
Away from the trains, it can be a little more complicated, and it's well worth knowing what your destination looks like in Kanji. A lot of the characters are used repeatedly for place names, like shima, bashi, yama etc. and it's worth knowing the points of the compass. When I say "knowing" I mean "write them down". You'll get to know some of them, but not at first.
Japan's also on Google street view, so if you're trying to find somewhere, find it on street view first. Buildings aren't numbered logically.
Back to the trains, on the Shinkansen platforms you'll see markings on the platform, which show you where to queue to get onto the train. The train doors always line up with these, so use them. Everyone else does.
With the JR pass, as has been said, you have to buy it outside Japan and activate it when you're there. It may not be relevant to you, but you don't have to activate it when you arrive. I was there for ten weeks with a three-week JR pass and used it somewhere in the middle.

I wasn't hugely impressed by Osaka but there will be plenty to keep you occupied for a couple of days. Hiroshima is great, however. Make sure you go to Miyajima. The view from the top is amazing on a clear day. And if you want to see a decent castle, Himeji's just West of Osaka.