This is the entire map of Japan here.
Japan seems pretty small in a world map but it is not that small if you live in or be there XDD.
My friend is traveling Tokyo to Aichi this time, so it will be this bid on the map he is traveling.
It depends on what is your priority on your trip that time I guess on what transport option you use.
Highway bus is a really good way if you want to travel cheap with certain distance.
Go to the site Willer Express and enter the info you need (traveling where to where and stuffs) on the left side of the screen where the red arrow is on the picture below. You will see the very reasonable price traveling long distance ;).
P.S. Adding some info on May 16th 2013 (today is my birthday by the way XD)!
Seems this company has even better deal.
Sunshine Bus Tour (in Japanese). Thanks for the link Robert!!