Will you fly out from Kansai Airport [KIX]?
Have you checked your accessibility to Haneda Airport [HND] in Tokyo?
Narita Airport [NRT] is actually outside Tokyo. A) Tokyo Wide Pass: Thursday: Narita Express to Tokyo proper B) Separate Booking: Thursday: Keisei Limited Express
Seats of JR Narita Express trains can be reserved.
Seats of Keisei non-liner trains cannot be reserved;
you cannot book your ride.
Maybe you are thinking about Keisei Skyliner,
where all the seats require reservation.
Arriving at NRT before the evening,
you highly likely can go
by low cost bus until Ginza then by subway to Shinjuku;
the total amount the fees is around 1200 yen per adult.
In the bus, you necessarily have your seat.
In the subway train(s), seats are secured on the first-come first-served basis.
- The Access Narita bus http://accessnarita.jp/en/home/#timetable-title-3386
For the other parts, B) sounds better.
Your traveling days include two weekend days,
when Nikko and/or Kawaguchiko area may be crowded.
JR Tokyo Wide Pass
cannot be used on both the 4th (Friday) and the 7th (Monday) of October,
which are normal weekdays;
its validity is for three consecutive days. Nikko World Heritage Pass
What destinations in Nikko do you have in your mind?
From Shinjuku you can make a day trip
to Lake Chuzenji area (Chuzenji Temple, Kegon Waterfall, etc.),
which is outside the validity of Tobu Nikko Pass (World Heritage Area). Metro to Asakusa
Tokyo Metro Asakusa Station (G-19)
is the east terminus of the Ginza Line;
trains arrive into either Track 1 or Track 2,
which is indicated on the train carfs body.
Asakusa Station of Tobu is a little away.
though five minutes might be too short,
ten minutes may well be enough to make this transfer.
- Map in Japanese
of subway Asakusa Stations (A-18, G-19)https://www.tokyometro.jp/station/yardmap_img/_station_%E6%B5%85%E8%8D...
: Arriving trains on the Ginza Line
run left to right on the map.
- Movie on YouTube showing transfer at Asakusa
from Tokyo Metro to Tobu Railway https://m.youtube.com/watch?v=YbOOIDYo8yg
: This movie starts from the Tokyo Metro station Track 2.