Thanks again to all who commented on my Tokyo list and questions - everyone's input was so helpful! I think we're staying in Hotel Mume in Kyoto. Here's a very rough preliminary list for Kyoto; please let me know if you have any input. Thanks so much!
Giro Giro (modern kaiseki)
Yoshiya (upscale kappo-ryori)
traditional kaiseki - very unsure; seems like every place has gotten mixed reviews!
vegetable - Isoya, Heikichi Negiya, Tenryo-ji Shigetsu
obanzai - Masuda, Waraji-Tei, Usui
tempura - Yoshikawa, Tenyou
kushiage - Wabiya Rakucyu Tei
yakitori - Wabiya Korekido
We probably would like to do traditional kaiseki for at least one meal, maybe a lunch...seems like all of the big names have gotten mixed reviews online so would be grateful to hear any recent experiences or thoughts...we're already working on booking a lot of expensive meals in Tokyo!