Itinrary 13 nights

Hi all,

I'm planning a trip to Japan for 13 nights.
7 Nights in Tokyo
3 Nights in Kyoto
2 Nights in Yamanouchi (Nagano)
1 Night in Tokyo (Returning for the flight)

On the way from Kyoto to Yamanouchi I'm planning to do the Magome and Tsumago Trail.

Any thoughts? Is this a good plan?
This is my second time in Japan, the last time I have been to Hakone, Takayama, Kawazawa, Nara, Hiroshima.