Booboostarz—we stayed in two places in Kyoto, both great. One was the Shinkoin Temple (http://www.shunkoin.com) which was clean, cheap, and very interesting. We got a tour of the temple, and we were able to participate in a Zen meditation class. It is part of a larger temple complex in Kyoto. I highly recommend it. 5,000 yen per person per night.
We also stayed at the Gion Fukuzumi (http://www.gion-fukuzumi.com/eng/) in the Gion district of Kyoto. It was a traditional ryokan, and we ended up with a huge room! We paid about 11,000 yen per person.
Enjoy your trip! I am, of course, envious. I do so want go back to Japan.
If you are interested, I’ll send you the URL to our photos.