There are a variety of accommodations available in Kyoto. Check the links below:
http://www.japan-guide.com/e/e623b.html Great all-round site, links to JR pass, Short term house rent, to Minshuku and love hotels.
http://www.kyotohostel.com/ – Kyoto Hostel / Ryokan around 3000Yen- Ryokan style hostel in Kyoto.
http://kyoto.j-hoppers.com/e_rate.html – thorough, professional, clean, cheap. Bunk dorms and Tatami rooms, plus.
http://www.travellerspoint.com/budget-accommodation-en-ci-645.html Long list of links to Hotels and Ryokans, some around Gion , Shijo, Teramachi.
http://www.japan-experience.com/voyage-japon/rent-a-house-in-japan/kyoto-houses Rent a house option
http://japanize.jp/ Rail maps, passes and timetables.
http://www.kyoto-ryokan-sakura.com/guestroom/guestroom_en.html – mid-market Ryokan, near Nishi Honganji.
http://www.travellerspoint.com/accommodation/34392-TANAKA-ya/ TANAKA-ya is located in Miyagawacho, one of Kyoto’s gesiha disricts. Very historical and elegant area!