What part of Japan? Although the country is "only" the size of California, there are LOTS of things to see & do while there, and depending upon where you're based, the choices will differ. (I lived in Japan May 1991 - May 1993, in Tokyo. I also visited there again in 2003 and 2007.)
One thing I'd suggest is to look into purchasing a JR Rail Pass (look online for it). These passes are only available to Non-Japanese, and you have to purchase before going to Japan. The cool thing about the pass is that you can pop onto any regular JR train just by showing the pass (which means that over time it will pay for itself), and you can take Shinkansen and some of the other "big" JR trains for only the reservation cost (THAT is where it'll pay for itself in no time). When traveling, stay at Ryokan instead of hotels because they're nicer and the room typically comes with dinner and breakfast... if you're still very young, you may also be able to stay in a youth hostel for some of your adventures.
Definitely bring an electronic dictionary so you can look up things that you can't read/understand (and so if you have difficulty communicating with someone, you can work with the dictionary to figure out the gist of what they want to tell you.)
