You can't get around Japan without JR!! (Japan Rail)

 The Railpass is a DEAL if you're going to be traveling roundtrips or long distances on the Shinkansen. The unfortunate part being that the Railpass can't be used on certain express trains. However, that being said, I believe one way tickets used to be a couple hundred dollars, so for about $271 a 7 day JR Pass that gets you anywhere is a steal. (14 day passes are also available)

Their website has been updated recently and includes all the info you need including schedules: http://www.japanrail.com/