Compare with the pass, how to find a single fare
Hyperdia perfect guide, train timetable and route search engine
If you want to build your itinerary by yourself, Hyperdia will help you a lot. This site is transportation search engine. You can search the timetables and routes of all trains, flights and airport shuttle bus. But this site is a bit tricky and too many functions and options to you. This guide will help you to find the way to use this site.
For non JR pass travellers. Guide to use JR single ticket, basic rules, validity and stopover
The train ticket rule is very complicated in Japan. But you may have to use the regular fare ticket because it is cheaper than the rail pass. This post explains you the basic ticket rule as easy as possible.
Guide to plan your trip. Fare Calculation
This post explains you the information about the fare calculation of the trains in Japan.