An immediate word of advice: if you're foreigner headed to Japan for a vacation, get a JR RailPass. Even if you're just moving around greater Tokyo everyday, it almost pays for itself -- and if you're getting out of the Kanto at all, it immediately is a great deal. It lets you ride any normal class (i.e., not green car) JR trains for free. You still need reservations on the Shinkansen. You need to show your passport with the tourist visa to get the RailPass, and you'll need to show the RailPass to the conductor on the train when you're using it for conducted trains (I think the conductor's theoretically supposed to look at your passport too). For JR lines around Tokyo, you'll show it at the window when you exit the station (you have to use the attended window).
If you haven't traveled by Shinkansen (or via France's TGV), you've gotta try it. Afterwards, you'll realize that trains can be an excellent way to travel!
