[konbini]

Kyoto is a must if you want to get a glimpse of traditional Japan.
Also a recommend a day in Takayama of Gifu prefecture. It is a lovely alpine town. Try fit in a night near Mt. Fuji. Hope you will enjoy your trip. Don't worry if you can't see and do everything you want. Once you see Japan for the first time, you will probably want to go back again.

P.S It is a great idea to learn a few basic phrases, most people will appreciate the effort.