Kyo-Yamato of Kyoto ?
Kyo-Yamato (京大和) seems to be a well-recognized and reliable place serving kyo-ryori kaiseki cuisine. The menu is highly seasonal and varies from week to week, or day to day, from what I get from their website. Whatever is included in the 50,000 yen course, I'm sure it's going to be exquisite. Be sure to take some photos and let us know how it goes.
You can navigate in English from the top right, but it's limited in the description, but it does have a reservation form.