Originally Posted by gbs1112

When I started this thread I wrote :
There is a free online website called Hyperdia, a rail planning application that is easy to use and right up to date. It provides not only train times and connections but also the exact cost of each ticket in whatever class you travel, including seat reservation costs. It even gives you all the arrival and departure platform numbers for your trains. If you print out your selected option the JR ticketing office can work from it with no language problems arising. Using Hyperdia you can easily calculate your exact rail costs and decide if the JR Rail Pass would be a better deal or if you will find a combination of rail and air ticketing is more advantageous. When you purchase individual tickets you can vary the class of travel to suit the circumstances and control the cost. Some of our Shinkansen sectors were very short, twenty to thirty minutes, and we chose standard seats while for the longer sectors we moved up to seats in Green Car (First) class. Standard seating is three plus three across and is a bit on the tight side for a well-built westerner. In the Green Car the seating is two plus two.
Hyperdia is even better and is an excellent tool for researching flights. It will point you to budget low cost carriers that sites like Skyscanner, Expedia etc do not bring up and will line up the relevant bus and train connections to link into those flights.