Get a 5 day or 7 day Japan rail pass. Validate it when you want to use it. As ww were going to Kyoto on the first day, we got it validated at level B1 of Narita airport. Book a train ticket from Narita to Kyoto via Narita Express 16 transit at Shinagawa to catch Shinkansen Hikari. Advised by the JR counter staff to change trains at Shinagawa instead of Tokyo as it was a smaller station and shorter distance to walk. No problems pushing our luggage as there were escalators.
We stayed at the New Miyako opposite Kyoto Station which was so convenient and easy to find. Clean, newly renovated, non smoking, pretty spacious and no frills. Across the road are lots of restaurants and bakeries.
We had a lovely meal in a tiny Japanese restaurant Gion Raku Raku introduced by a friend. Only 3 guests and another lady came in at around 8pm as she works in Tokyo.