If you decide to fly to Tokyo then getting a JR rail pass before you travel is definitely going to be a good decision in terms of value and allows you unlimited travel on JR trains and all but the fastest Bullet trains. If you only want to go to Kyoto then you can buy a pass at KIX airport station that gets you a return to Kyoto on a reserved seat train.
If you do fly to Tokyo - I recommend arriving at Haneda, it is much more convenient than Narita.
There are many flights between Haneda and Itami (Osaka city centre airport) and from there it is easy to get to Kyoto. Using BA avios for this route is really good value. 4500 one way and about 3 GBP in taxes.