After a long discussion with Mrs. NU and a few phone calls here is what we are thinking,

We arrive in NRT at 5pm from PVG on ANA on the 18th, so first I will change that so I arrive 3:15. We will stay at the Four Seasons Marunouchi for the proximity to Ginza and the Tokyo station. Then on the 19th in the afternoon take the Nozomi to Kyoto and then fly home from KIX on the 21st.

Leaving the following questions,

Will I have problems getting to the train station from the Four Seasons with all our bags?

What about hotels in Kyoto?

Again thanks for everyone's help,
N.U.