How to transfer from Tokyo Airport

Once you collect the bags, go to the exit and follow the signs to the Train Station (JR = Japan Rail, be careful because there are other private companies that are not included in the Rail Pass). Before entering the train station, go to the "Travel Service Center" or "Ticket Office" and say you want to change the "Exchange order" for the Japan Rail Pass.
They will make you fill out some forms and give you all the information you need.
Remember that it is the best time to book train tickets for the entire trip! Try to search the hours on the internet and bring them with you.
Then enter the train station and take the Narita Express to Tokyo Station: YOU MUST HAVE YOU TICKET WITH A RESERVED SEAT! You have to ask for this ticket at the Ticket Office when you change you exchange order.
Follow the signs to the station and you will arrive quickly. Show the ticket and the JRP to the operator that you will find at the entrance (it is not possible to enter through the automatic doors). This journey takes 1 hour and is covered by the JRP.

Once you have collected the bags, go to the exit and follow directions to Tokyo Monorail.
To get the Japan Rail Pass (in exchange for the exchange order) you have to go to the JR EAST Travel Service Center office which is located in the monorail station (open from 07.45 to 18.30 h).
They will make you fill out forms and give you all the information you need. Remember that it is the best time to book train tickets for the entire trip! Try to search the hours on the internet and bring them with you.
Take the monorail (you just have to show the JRP to enter).
Get off at Ginza station (20 minutes, 490¥ , including the JRP). Here you have to change to the JR Yamanote or JR Keihin-Tohoku Line to Tokyo Station (5 minutes, 160¥ , including the JRP).

Take the Narita Express to Tokyo: YOU MUST HAVE YOU TICKET WITH A RESERVED SEAT! You have to ask for this ticket at the Ticket Office when you change your JRP exchange order.
Follow the signs to the station and you will arrive quickly. Show the ticket and the JRP to the operator that you will find at the entrance (it is not possible to enter through the automatic doors). This journey takes 1 hour and is covered by the JRP.
Once you arrive to the Tokyo station, follow the signs for "Shinkansen" until you see the bifurcation between "blue" and "green" lines. Take the blue one and show the ticket and the JRP again.
Just there you can see a screen where the platforms for different trains are indicated. Follow the one that you ticket indicates.
The train to Kyoto takes a little over 2 hours (between 130 and 140 minutes depending on the train).

Take the monorail (you just have to show the JRP to enter).
Get off at Ginza station (20 minutes, 490¥ , including the JRP). Here you have to change to the JR Yamanote or JR Keihin-Tohoku Line to Tokyo Station (5 minutes, 160¥ , including the JRP).
Once at Tokyo station, follow the signs for "Shinkansen" until you see the bifurcation between "blue" and "green" lines. Take the Blue one (you will have to show your ticket and the JRP again).
Just there you will see a screen where the platforms for different trains are indicated. Follow the one that your tickets indicates.
The train to Kyoto takes a little over 2 hours (between 130 and 140 minutes depending on the train).