You might try someone like Hostelworld. They have all types of hotels including Ryokans, you can pick something in your price range / location. I've used them for 2 trips to Japan, you pay a small deposit to book online, then the balance when you arrive at the accomodation. It does reduce your flexibility with your plans though, but as Troo says, you are going at quite a busy time.
Hostels in Kyoto - Book Online at Hostelworld.com
Have a great time anyway,
Kevin