If OP go the other direction on Chuo line, he can get to Nagoya then onward to Kyoto. Probably the cheapest way to Kyoto on train. Going that direction in the morning will be no problem at all.
He can even stop off on the way to see the Matsumoto Castle.
Seriously, to OP:
If you have luggage and are taking Yamanote line to Shinagawa Stn., take the last few cars since the elevators at this station is on the south end of the platforms.
If you are taking Chuo line into Tokyo Stn, you want to take the first few cars since the elevators at Tokyo Stn is at south end of the station.
In both cases, you will have to cross the entire concourse since Shinkansen platforms are at the other end.