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Travelling by Train
Travelling by train is a great and 99.9% of the time extremely time efficient way to see Japan. The only drawback can be the price, but this is made up for by the speed and frequency of the service provided.
You will be able to get by in most situations with very little Japanese, as long as you know the name of the station you want to travel to. Almost all stations, even those in deepest darkest inaka have the name of the station written in both Japanese (kanji and hiragana) and roman letters. Each stop also has signs visible from the train which tells you what the stops on either side are called. So unless you fall asleep, missing your stop shouldn’t be a problem! Most large stations also have a good amount of English on the signs, so you can find the ticket office, waiting rooms and toilets very easily! Timetables are usually also displayed with English translations. If you are travelling by express/shinkansen trains, look for the signs on the platforms which tell you where your coach is. Once on the train, carriage and destination information is usually displayed in English too. All in all a very stress-free experience!
At most stations you will have your ticket stamped before you are allowed onto the platform, so you can ask the man who stamps it which platform the train leaves from: “nan ban desu ka?” or if you are able to read kanji, check out the information boards.
Be aware that some trains will split at some point in the journey (occasionally on the shinkansen back from Tokyo), so make sure your carriage is going where you think it is! Usually the conductors will point you in the right direction if you ask them. Of course, if you have a reserved seat, you don’t need to worry about this.
For cheaper travel, the Seishun Juhachi Kippu (Youth 18 ticket) allows you to travel practically anywhere in Japan very cheaply (2300 yen per day)! You buy them in a sheet of 5 tickets (11,500 yen in total) which can be used on 5 consecutive or non-consecutive days. You can even split them with a friend! However this is a seasonal ticket that is usually only on sale during vacation periods. Check out this site for more info, details of night trains, schedules and advice on route planning. http://www.geocities.com/TheTropics/Cove/5750/local.html#18kippu
By far the most important website for your time in Japan will be http://grace.hyperdia.com/cgi-english/hyperd01.cgi . From there you can access a page where you can enter your route info and it will come up with a selection of route and price options for you. Marvellous!
Apparently the most up to date special deals are in the back of the train timetables book which is available in most bookshops. Ask a Japanese friend to help you translate!