Hi Again,
I was just re-reading my previous post and see that I made a couple of grammar mistakes, so sorry for that!
Going on with your questions:
There are some very nice tickets that you can buy in Tokyo to save money on transport and travel freely around the city. My personal favorite is a one day Tokyo Metro Pass which is just 710 yen and allows for unlimited travel on the Tokyo Metro for a given day.
In addition some other day tickets are available that you may find useful, including a day pass that allows for unlimited travel on JR Lines in Tokyo, you can read more about them here.
I would try to be at Narita Airport at least two hours before departure. This because it of several factors that can take up some time (including pre-boarding baggage inspection) and you don't want to be late! From Kyoto take the Shinkansen to Tokyo station and transfer here to the Narita Express to Narita Airport.
Regarding seat reservations, trains rarely sell out and you get reserve seats up to 5minutes before departure. Basically this means showing your JR Pass to the staff and telling them where you would like to go. Than they will print the tickets for you and you are ready to ride! You can of course also make seat reservations if advance if you prefer.
I hope this helps!
Daniel
PS: Public transportation in Kyoto other than local JR lines is not covered. Something that offers great value is the one day bus pass that is just 500 yen and allows you to take the bus anywhere in Kyoto. A normal bus ride costs 220 yen so you will be sure to make savings quickly. Also buses are the best way of public transportation in Kyoto as they go everywhere! However if the weather permits, consider exploring Kyoto by bicycle. You will encounter many great places, that you will otherwise miss.