Another option not mentioned is to travel from Kyoto to either a hotel in Tokyo or near Narita the evening before. One thing about the shinkansen trains is that it is difficult to travel on them with a lot of luggage as there is not much room to store it. Instead have your luggage forwarded from Kyoto to your Tokyo hotel the day before keeping only what you need for in carry ons. Ask your hotel in Kyoto and they will take care of calling a freight service. The cost is about $20 a suitcase. Enjoy the day in Kyoto and take a later train the day before to Tokyo. You are not going to be able to do much in Kyoto the morning of your flight anyway with an early evening departure. You can then enjoy dinner in Tokyo and have time in the morning to do something in Tokyo as well. Then around noon take the airport limosine bus (picks you up at front door of most Tokyo hotels - arrange with your concierge) to NRT or take the NRT express train. If you are a wary traveler or if you have a lot of luggage, then stay at a hotel in Narita. In the am go to Narita town for a few hours before heading to the airport.