Hi,
One suggestion is to stay in Japanese style hotel, called "Ryokan" where you
can experience with typical Japanese style room and bed, etc.
Check
http://www.ryumeikan.co.jp for more information of your stay in Tokyo.
You can start with your room rate at Yen 10,000 or about $100per night.
It will be a great opportunity to be in this side of the world. This hotel has an English page for foreign guests.