Can your mother contribute any money to the kitty?

I think that you are correct in saying that low-cost accommodation is best booked in advanced.

http://gojapan.about.com/od/ryokan/t...n-in-Tokyo.htm
http://www.planettokyo.com/hotels/in.../detail/ID/58/

I can't vouch for either of these sites but some backpacker-type friends of mine do so take that for what it is worth.

What is your preferred area? Price range? Are you willing to stay further out but take trains in order to save some ¥?