I cannot recommend getting the Japan Rail Pass enough for your trip to Japan. It greatly simplifies your intercity travel, is easy to use, and gives you the most flexibility for your trip. Furthermore, I managed to save a good amount of money (to be used instead for all of the great FOOD of course), by using the JR Pass on the longest parts of my trips. To order one yourself, click on the links below and choose between 7, 14, or 21 day pass in 1st or 2nd class.