Good manners is what they have there. But, with that said...riding the subways and such, they are VERY pushy to get on and off. They don't say "excuse me" when they bump into you. They just bump and go.
Japan is a beautiful place. I loved visiting there and seeing the culture. I will tell you tho...traveling thru the country, it is a bit on the expensive side.
Just do your "homework" on Japan and you'll be fine. My biggest advice for you would be to get in touch with Youme and ask her questions. There's also another lady, Gaijin, I think her name is. I'm sure both of them could help you out.