Kyoto is famous for tofu, how about a tofu course lunch? Tousuiro was a great experience for me. They have two shops. I don't think you can count on English being spoken at the restaurants, but their website does have English, sorry, not sure if you can speak Japanese.
Thank you everyone for your help. I think a Tofu lunch is a great idea- though not sure my wife will enjoy it! Is Kyoto famous for tempura, I am going to Tokyo afterwards and have a reservation at Kondon.
IN Tokyo I also have a table at Hishinuma and will also try to eat at Sushi Mizutani and Sukijabashi Jiro. I also want to eat at Birdland.
I dont speak Japanese - though the wife speaks a little. I've managed to make reservations so far either by calling the restaurant directly or through my hotel. Interestingly I found that people speak better English in Kyoto than Tokyo.
Are you only looking for kaiseki-type places? So many kaiseki-style meals in a short period of time can get rather monotonous--same season, same ingredients. Preparations may differ, presentations certainly will, but there's really only so much you can do within a traditional Japanese framework (in my opinion).
Would you consider trying tempura in Kyoto? I really like Ten-you, owned by the Tawaraya people. Tempura Yasaka Endo is also supposed to be quite good, but I haven't been there, yet.
I am a big fan for Tankuma Kitamise and Chef Kurisu. He has written a beautiful cookbook about his cooking (in Japanese).
Also, not sure if they are open for lunch, but Kikunoi with Chef Murata and Kitcho with Chef Tokuoka. They have a nice cookbook out on Umami and Dashi (in English).