Stay at the guest houses.
When we stopped in Kyoto along our Shinkansen S-N self made tour,
we found one for about 2500 yen. This had shared wash room & bath room,
also shared bed room, but it saves a lot of monies.
Plus you get to meet people from all over the world at these places, if you want.
Or just a cheap place to stay.
The places at the link Hiroyuki Nagashima posts are for similar rates,
not all shared rooms.