I completely love Japan. I lived in Osaka for a year, and if it weren't for DH, would probably still be there. I don't know Tokyo very well, though there are other people on the forum who have lived there, so hopefully they'll be along later. However, if you like Japanese art, I would recommend the Japan Traditional Craft Centre. It's expensive, but has beautiful, beautiful things. Also, I'd suggest going to Harajuku to see all the teenagers decked out in their costumes. Oh, and be sure you're adventurous and open minded about the food. It's delicious, but definitely not what you're used to, especially if you'll be in a small village. It won't be posh sushi of the sort you get outside Japan. But if you keep an open mind, you'll be surprised what you end up liking.
Have a great time!