Japan is a place like none. Expect to be greeted with hospitality and warmth wherever you travel coupled with convenience of great public transport. Language might be a problem even in big cities so be prepared to communicate through signs and pictures. Food is interesting, tasty and too pretty to eat at times but for vegetarians - beware because Japanese consider even seafood to be vegetarian. Do your research on restaurants where you can find veggie food.
3 days in Tokyo - Visit all the top tourist attractions but for a different experience let yourself wander through streets of Akihabara to see the 'weird' side of Japanese pop culture and fashion. And make sure you visit a karaoke bar! Book a JR English guided tour to Mount Fuji - well organized and worth every penny!