For a ryokan, have you considered doing a side trip to Hakone/ Mt Fuji? You can do that on your way from Tokyo to Kyoto. Lived in Tokyo for 2 years… you mentioned a lot of nice spots. Hoshinoya in Kyoto can also provide a nice experience.
Do you like shopping? There are a lot of cool local stores that sell pottery and japanese ceramics. Tokyo Midtown has a nice shopping mall with some traditional stores selling handicrafts that make great souvenirs. Do check out some fun neighborhoods Naka Meguro, Azabu Juban, Omotesando/ Harajuku neighborhoods.
Have fun! Don’t forget when taking cabs you don’t need to open or close the doors. The drivers hate that. Just let them open and close (automatically) for you. Also, if navigating the subway system, make sure you know what exit you are exiting as exits can be whole neighborhood blocks away, even though the subway station is the same.