You can easily navigate most of Japan with nary a word of Japanese. Almost all the train stations have signs in English. Even the train ticket machines have English menus. You might want to invest in a Rail Pass
if it's worth the value (depending on where you want to travel and the duration - find the train routes and prices here
). You can also invest in regional passes. Otherwise, a Suica or PASMO card would be nice to quicken the process. If you are on a budget, you can utilize the service of overnight/long distance buses (like ones from this company
) to travel long distance.
You would also find Tourist Information offices in all the major stations with English-speaking staff, maps in English and other useful information. In major tourist areas like Kyoto and Nara, you would also find huge maps in English placed on the streets and tourist information offices in various locations across the city.
It pays to plan. You would find a huge amount of information in English and many useful electronic maps on the Internet. Check out the Practical Travel Guides on JNTO website
I found the buses to be a bit tricky at first but you would soon learn how they work (slightly different in Kyoto vs Tokyo). For getting around Kyoto's landmarks, you might want to purchase a 1-Day (or more) Bus Pass (from the office located just outside the the north exit opposite to Kyoto Tower).
Useful link for Kyoto buses: http://www.city.kyoto.jp/koho/eng/access/transport.html
It would help if you have a data plan so you can access Google Maps on the go. Location of buildings and attractions can be a bit tricky at times. This would also be useful to access websites like Hyperdia on the go so you can reschedule your train travel time. Otherwise, always have a backup plan for the train departure time (although you would only wait a few minutes in most stations if you missed your original time; provided it's not the last train, of course)... this is more important if you are connecting trains.
Carrying a phrasebook, a guide book (I would recommend Japan by Rail
) and a map would also help.
Useful link: http://www.customs.go.jp/english/summary/passenger.htm