Honeymoon trip From Narita airpot to Fuji

Tokyo Station Hotel would be lovely for a night or two of honeymoon, surely.

Or the Prince Sakura at Shinagawa.

You'll be at either in the blink of an eye, on the Nex, compared to a taxi to Mt Fuji.

And either way, easy trip to Osaka when it's time to go.

Whatever you choose, have a wonderful time.

Sultan:
Arrange earlier flight, from AUH ( airport in Abudhabi, 1 hour from DXB) to Narita..

That sounds a good choice.
(Direct flights from DXB to HND | NRT seem not timed well for well for you.)

Then, your inbound flight is
Etihad EY878
: AUH (11/28 22:15) -- NRT {T1 North} (11/29 12:45) (9 hours 30 minutes).

LikeBike:
at least don�ft go to Fuji first.

I disagree.
Generally winter is a good season to see Mount Fuji.
Replacing Kawaguchiko by Hakone can shorten your traveling time.

Sultan:
Checkout 3rd December from Hoshinoya Kyoto and go to KIX and then reach Honolulu 4th December!

You reach Honolulu before the date changes,
departing from KIX in the night and arriving at HNL in the morning or around noon;
this flight is estimated to take about 7 and a half hours.
https://www.kansai-airport.or.jp/en/flight/kix_scheduleresult

Ask/Request an airport pickup from HOSHINOYA Fuji hotel.

Hoshinoya Fuji is more than 100 kilometers away from NRT.
Now you plan to arrive early enough
to go by railway and bus to Kawaguchiko Station.

Narita Airport Station (in NRT Terminal 1) and Shinjuku Station
are connected by JR Narita Express [N'EX].

N'EX trains leaving NRT mostly have two destinations,
get divided into two trains at Tokyo,
only one of which runs for Shinjuku.
Please make sure to get on the correct car.
Your train number, car number and seat number
are printed on the front of your reserved-seat ticket.

Alternatively,
you can travel a little faster
by Keisei Skyliner until Nippori
then by JR Yamanote Line Inner Loop to Shinjuku.
Or, you might hope to make a side trip to Ueno
(Narita Airport to (Keisei) Ueno then (JR) Ueno to Shinjuku),
though you may get there too late to visit the zoo.

- JR East Travel Service Center (Narita Airport)
https://www.jreast.co.jp/e/customer_support/service_center.html
: Here you can purchase
JR basic fare tickets
to get from Narita Airport to Shinjuku
and to get from Mishima to Kyoto City Area,
JR reserved-seat Limited Express ticket for your Narita Express ride
and JR Shinkansen (super-express) reserved-seat ticket
for your Hikari ride from Mishima to Kyoto.

Shinjuku and Kawaguchiko are connected by expressway bus.
https://www.highwaybus.com/gp/inbound/index?lang=EN
: Select "Tokyo" and "Yamanashi" then search.

Shinjuku Expressway Bus Terminal is in Busta Shinjuku,
which is near the New South gate of (JR) Shinjuku Station.

JR Narita Express trains from NRT
arrive at Track 6 of Shinjuku Station.
You go up to the bridge,
and pass through the New South exit gate.
Then, you walk to Busta Shinjuku and go up to the 4th floor.

- Maps of (JR) Kyoto Station
https://www.westjr.co.jp/global/en/timetable/pdf/station_kyoto.pdf
: On the first / second map, the north is to to the bottom / the lower right.

Arriving at Kyoto Station by the Shinkansen,
you go down to the concourse
and pass through the Shinkansen Central Transfer Gate,
where your Shinkansen reserved-seat ticket is collected
and your basic fare ticket (to Kyoto City Area) is returned.
(You keep this basic fare ticket until Saga-Arashiyama.)

Then you cross the bridge
(above the conventional (= non-Shinkansen) tracks),
getting down
to around the joint of the two platforms for Track 0 and for Tracks 30 to 34.
Haruka trains for KIX mostly depart at Track 30.
Trains for Saga-Arashiyama depart at Track 31, 32 or 33.

You can visit the JR Ticket Office beside the Central Gate,
being still inside the gate.

In any of the two cases (a) and (b) shown below,
to make a stopover at Kyoto Station on your way to KIX,
you need tickets separately until and beyond Kyoto.

(a) You do not reserve Haruka seats.
The Haruka discount ticket (Kyoto Area, 1600 yen) is suitable,
which can work as a one-day, one-way ticket
to get from Saga-Arashiyama or Kyoto to Kansai-airport.
https://www.westjr.co.jp/global/en/ticket/icoca-haruka/

(b) You reserve Haruka seats.
A basic fare ticket and a reserved-seat ticket are necessary.

I would scrap one or the other. You will waste an entire day traveling from Hoshinoya Fuji to Hoshinoya Kyoto. It's not like you get on one train for six hours and your there. There are three to four transfers depending on how you go about it. Once you arrive at Kyoto station, you have to get on a taxi for another 30 minutes. Which leaves you only one full day to actually see Kyoto. Your original plans were to go to Kyoto only. Why not fly into KIX and reserve a room at another hotel in Kyoto for the first two nights. I am sure there are other luxury accommodations that will suit your needs. Although, Hoshinoya seems to be next level. The other option, would be to stay at Hoshinoya Fuji and then stay in Tokyo the last two nights. It is a good time of year for viewing Mt Fuji and the view from the hotel looks epic. Also, since you are so intent on staying at this chain of hotels, there is a Hoshinoya in Tokyo, that is centrally located in the city.