Which ticket for couple days in Tokyo

Hello there,

I would like to ask you what type of tickets we should use for our itinerary. We plan to buy 14days JR pass and start it by our trip to Nikko. But I am not sure what we should use for the way from airport and first days in Tokyo, Same problem we have for last couple days in Tokyo before our departure. Is there some 1/2/3 days ticket which also cover way to airport? What about Suica or pasmo card?
Thank you in advance for your recommendation.

Mar 24 Arrival to Narita -> Tokyo (Shibuya)
Mar 25 Tokyo
Mar 26 Tokyo (trip to Nikko)
Mar 27 Tokyo
Mar 28 Tokyo -> Fujikawaguchiko
Mar 29 Fujikawaguchiko
Mar 30 Fujikawaguchiko -> Kjoto
Mar 31 Kjoto
Apr 1 Kjoto
Apr 2 Kjoto (trip to Nara)
Apr 3 Kjoto
Apr 4 Kjoto (trip to Osaka)
Apr 5 Kjoto
Apr 6 Kjoto -> Hiroshima, Miyajima
Apr 7 Hiroshima, Miyajima -> Fukuoka
Apr 8 Fukuoka -> flight to Okinawa
Apr 9 Okinawa
Apr 10 Okinawa
Apr 11 Okinawa
Apr 12 Okinawa
Apr 13 Okinawa -> flight to Tokyo (staying in Shinjuku)
Apr 14 Tokyo
Apr 15 Tokyo
Apr 16 Departure from Narita