How can I get from Narita Airport to Kyoto or Shiga?

My plane will arrive in Narita Airport at 3:55 PM in late July. I will be staying in Shiga prefecture, but I might be able to stay in my girlfriend's house in Kyoto if it would be too difficult to get to Shiga from the airport upon arrival. What would be the cheapest way to get to either Kyoto or Shiga, while making it before 11:00 PM?

ALSO, I will have to return to Tokyo for the Summer Sonic festival 10 days after my arrival, and we might stay there for 2 or 3 days. I have heard of the JR pass, but those are sold by 7, 14, and 21 days. I will be staying in Japan for about 45 days. I will only use the train in the first two weeks ( Airport>Kyoto/Shiga>Tokyo>Kyoto/Shiga) and again when I have to return to the airport (I do have to commute to Kyoto from Shiga 3 times a week, but i believe that's inexpensive).
I also have a choice to change my flight to arrive and depart from Kansai for $250+the fare difference. What would be the most affordable way to go about this?

Take a bus. I've been in Narita two years ago, just take a bus or taxi.

It would be easier if you used Kansai Airport since it is closer to Kyoto, also it eliminates the need for you to travel from Narita Airport to Tokyo, then Tokyo-Kyoto-Tokyo-Kyoto then back to Tokyo and on to Narita Airport (narita airport is 1-1.5 hours from Tokyo) over again, you waste a lot of time and hassle don't you think?

Fly into Kansai go to Kyoto (very cheap by train or bus), go to Tokyo for the sonic vestival then back to Kyoto sounds a lot easier and less hassles right!

just take shinkansen

I highly suggest picking up a copy of the latest Lonely Planet - Japan book.

This book has all pertinent information on not only your transportation options, but accomodation, food, entertainment, shopping, and more.

Most people would opt for the train from Narita to Tokyo, then Tokyo to Kyoto. That could get expensive, as the most convenient way is the shinkansen (bullet train), which is expensive.

I think it would be easier if you just flew into Kansai. Getting to and from Tokyo is going to cost you like $200 each way, and all the time too.

Just bus it or take local trains to Tokyo for the festival. That lets you see the countryside too. Your gf in Kyoto should be able to figure that out.