Two of the seasons that are very busy in Kyoto for Japanese tourists are cherry blossom season in early April and fall color season in early November. Your dates are right in the prime time for fall color viewing so many Japanese will flock to Kyoto and often have reservations a year out. It is also possible that some of your choices are simply not booking a year in advance. I'd try again after the first of the year and again at the 6 month mark.

For rooms for two people in the $100.00 range, you are going to have to look at business hotels. Try: http://www.japanhotel.net/area.aspx?area=KYOTO .

Another idea is a nearby city. With a Rail Pass, commuting a short way is no problem. For example, I checked Comfort Hotels and found the one in Kyoto unavailable for your dates but the one in Nara has availability in your price range. I have done that in the past, staying in Nara and riding the local commuter train each morning to Kyoto, Osaka, Hikone, etc. Nara is very quiet at night but quite beautiful and the Comfort is a 2 minute walk from the JR station. The Rapid service runs every half hour or so and takes 47 minutes to Kyoto.