An inexpensive, comfortable and clean place to stay in both Tokyo and Kyoto is the K's House. The staff there are multi-lingual and are very knowledgeable about the area. The K's House in Kyoto also has an all-you-can-eat buffet breakfast for about ・700.
In Kyoto I strongly recommend visiting the town of Ohara in the mountains to the north of the city (only requires train fare and bus fare to get there). Ginkakuji (the Silver Pavillion), Fushimi Inari Taisha and the Arashiyama Monkey Park are my favorite sites in Kyoto.
For more information about things to do and places to stay and what they cost, I recommend browsing wikitravel Kyoto and JapanTravel.com
I've gotten most of my information about traveling in Japan from there