You're going to want to activate that JR pass on 4/5 if you want it to still be good on the day of your departure.
Also, make sure you give yourself enough time (four hours, rounding up) to get from Kyoto back to NRT:
https://www.kyotostation.com/traveli...ional-airport/
Take the Hikari to Tokyo or Shinagawa and then catch the Narita Express to, uh, Narita, and per ANA, you want to be through check-in an hour before departure.