Thanks for all the replies! I never consider the Tolls Japan until you guys mentioned it.

At this point, I think I am more convinced to ride the train. I will talk to my friends about it. I am now thinking that we should buy the Japan Rail Pass for 7 days, and after that, maybe get a rental car for a couple days if we really want to.

Anyone bought the JR Pass before? Did you get the Green or Ordinary?
http://www.japanrailpass.net/eng/en003.html

Thanks for the help, Flyertalk!