Ooo, yay!
Buy a JR Rail Pass before you go. Since you’re going all the way to Hiroshima and back, it will be worth the money: http://www.japanrailpass.net/eng/en001.html
Get a Suica card for the private-line trains – and, for that matter, these days you can buy a lot of things with them: http://www.jreast.co.jp/e/pass/suica.html
For route-planning – also handy for checking the cost of tickets: http://www.hyperdia.com/
This might be a bit self-evident, but make sure you at least learn the kanji for major place names you intend to visit, so you can read them on signs in the off chance there’s no English or hiragana. For example, 広島, 新宿, 秋葉原… 神戸? Et cetera.
Don’t bring too big a suitcase – if you’re going to be travelling with it, and need to put it in station lockers, bigger lockers are more expensive and harder to find. On that note, the lockers always take hundred-yen coins, so don’t spend them all. Also, on the trains, you’re better off with a wheeled suitcase than a backpack.
Take photos for us. =D