Please see my Mt.Fuji trip plan(2days trip), and give some advice.

* the most early bus from hotel leaves at 5.47 and arrives at 7.02 at Tokyo Station.
> GOOD! I hope no big delay!

* i take the Marounouchi subway Line from Tokyo St to Shinjuku Station
> How about using JR line?
I am not TOKYO people but I think JR line looks easier.
I think many JR train going to Shinjuku.

* At Shinjuku Station EXIT West OR EXIT A12/A14 underground passage ?
> According to the web site of “Shinjuku bus terminal”, you are right but go WEST.
https://www.highwaybus.com/html/gp/foreign/en/access/
If you are using JR line, also go to west to reach Shinjuku express bus terminal.

* to Shinjuku Expressway bus terminal OR Keio Highway Bus Terminal ?

> it is actually the same, but Shinjuku busterminal is more familier for many people.
Just go to Shinjuku bus terminal.

* i guess i need to take the 8.40 bus although I arrive at 7.02 at Tokyo Station and 40 min I won’t make it.

> Yes, better to take enough time. From Tokyo to Shinjuku, is about 15-20minutes.

* can I book the bus at highwaybus.com ? OR is there another website i need to book ?
here you can book, your bus. in English.
TOKYO- Mt.Fuji 5th station

https://www.highwaybus.com/rs-web01-prd-rel/gp/foreign/frgSelectLine?lang=en

* arrival at 11.00, pay fee 1000¥
> yes, entrance fee
you might get an suvenior.

* start climbing at 12.00
> OK

* arrival Toyo-kan 16.00
> HOpefully!

Start climbing to summit 23.00
> GOOD! I hope your sleep a little.

* arrive exhausted at summit at 3.30 and thank you for your help & Njoy 😉
> I think so! very tired

* is it possible that you book a room in Toyo-kan a small room on Monday the 6th of July?
>I called to TOYOKAN and they said you can only book an Large room because you are alone.
Large room can be booked.

* is the dinner included ? I read the small room is 10.000¥ incl breakfast & diner. I need to pay cash at the hut 10.000¥ ?
> Yes, dinner and breakfast(looks like an lunch box).
And you are required to pay by cash.

* what do you think about clothing : winterjacket or layers of clothes ? Because i guess it will be hot at the 5th and freezing at the top.
> I think you better bring an fleece jacket or sweater like stuff.
And some rain jacket.
I heard the wind is very strong there so you better prepare yourself for stong wind and rain.
I think it is actually easy if you are in AMS.hahaha.
I have my packing list here so please use it.

http://mtfujirental.com/equipmentmountfuji/
Packing list

I hope this helps you prepare more.