Johnnie Hillwalker or Mr. Hajime Hirooka has been doing this walking tour for 15 years. You can find him in Lonely Planet under the Kyoto section.
Pay 2000 yen and walk 3 kilometres for 5 hours. He doesn’t take us to tourist spots, instead he takes us to active temples and shrines where Japanese people go. He takes us to see home industry in the old streets of Kyoto where they make paper fans, tofu, tatami, pottery, etc. We also go to the old geisha area in Gojo where the art of geisha is not as prosperous as before. It may seem not as exotic as the media always portrays, but that is the reality in Kyoto. Along the way Johnnie also tells us the history of Japan, in particular the places we visit.
I highly recommend Johnnie’s Walking Tour. He goes every Wednesday and Friday. There’s also a similar tour every Monday but with other guides.