Easiest way is to take the bullet train from Kyoto to Tokyo and then connect to the Narita Express train from Tokyo to the airport

Train ride from Kyoto is about 2.5 - 3 hours, give yourself 15 minutes to connect in Tokyo (it's a fairly long walk from Bullet train to Airport Express) Airport express is typically just over an hour.

If you are planning on a two hour advance check in, going the morning of may be a challenge. You may be able to find some inexpensive accomodations near the airport or in the town of Narita