You'll need to take the Narita Express to Tokyo station and change to the bullet train. Try to travel fairly light and allow extra time, and remember the trains in Japan are expensive. I almost missed a flight out of Narita coming from Kyoto because I underestimated how long the trip would take. It would be far easier to fly into Osaka as there is a direct train from Kansai Airport to Kyoto that takes about 80 minutes.