There is a recommended itinerary on Page 1 Post #1. You can use it as reference.

In terms of your Mt Fuji - what does it mean "hike from 5th to 6th station"? What is there @ 6th station? The climb is usually from 5th to 10th station if i'm not mistaken and you can only climb it in Summer (usually July). Or is this a hike via the Yoshida trail?

Good idea on Mt Takao, it's very beautiful and it'll be a refreshing hike. I recommend to take the chair lift as it's pretty fun.

Your itinerary is very concentrated in Shibuya and Shinjuku only. There's a lot of places you can visit.

Looks fine to me. You can actually make reservation for the bus trip (Shinjuku-Kawaguchiko) earlier online if you wish (not need CC or pay first).

For the Hakone-Shinjuku train part, you can pay slightly extra to take the faster Odakyu Romancecar

EDIT
You might want to check how are you going to Odawara? Don’t think the pass cover it

Yes. You are correct. When you buy the pass, i think they will ask how are you going to take the route i.e. highway bus first to Kawaguchiko or train first to Hakone.

Unless u are travelling on Golden Week, I don’t think Romancecar will be fully booked. You can purchase it on the spot

Definitely one night in Fuji. You don't want to miss Mount Fuji during sunrise. It's also your best chance since there will be less fog in early morning

Well, if you want hassle free. Buy a new Digi Prepaid online, Rm8, reload the amount of credit base on how long you visit japan. Rm25 for 3 Days Roaming come with 2GB + 30mins voice call. 9 days visit in Japan just cost you Rm75.

i will totally do that, just wan to walk around doing absolutely nothing and onsen. a relax trip.

but...
normally ppl bought fuji hakone pass... 3d2n
mean they will do fuji gotemba hakone tour

Just used it last week in Tokyo for the last 3 days when our AirBnB only got fixed wifi.
Easy to activate and use.  Don't turn on Data Roaming first.  Dial *800#. Type 3 and reply, for the 3-Days/RM25 package.  Will receive a successful sms.  Turn off auto select carrier, manually select either Softbank or docomo.  Turn on Data Roaming.  Walah ...
Can check the data balance using MyDigi app.

https://new.digi.com.my/roaming/roaming-pass

yes, the pass entitled u....

1 way ride from Tokyo to Hakone, and 1way back... ☒
but with condition, hv to do 1way travelling by train and 1way by bus.
it doesn't matter u choose to ride train or bus first.
u can also upgrade ur train to romance car(actually train)

unlimited pirates ship ☒

unlimited tram and cable car at gora ☒

unlimited bus at kawaguchiko/gotemba/hakone ☒
note: only bus operate by Odakyu {mean no tour bus for kawaguchiko lake tour)

tips: it is Very Important to book the return ticket in advanced, else u might not able to come back... Coz the return ride always full.

By the way, I got two AirBnB Experience coupons worth USD100 each, valid I think until December.  I didn't use them in my recent trip.

Got them from Japan AirBnB cancellation after June this year ... not sure whether they're tied to my AirBnB accounts, hopefully not and maybe they aren't only for Japan AirBnB experience; tho I prefer to see them being used by visitors to Japan.

Here they are:-
B84FH2KJ (redeemable until December 15th)
KHNCZPRM (redeemable until December 19th)

By default, my Digi will switch to Softbank ... without data roaming, just normal voice and for receiving sms. 
After subscribing to the 3days-RM25 package, it says there can choose between Softbank or docomo ... I'm kinda biased towards docomo, so I used that lor, but I think can switch anytime to Softbank as well.

The coupons, first come first serve lor ... USD100 value for AirBnB experience maybe only enuf for 1 person or 2ppl ... if group, sure need to add more.  Don't think can use 2 coupons for the same AirBnB experience.
Let us know here if you've redeemed them, so that others no need to try oredi.
Agreed ... onsen experience in Japan is kinda must ... don't know why some are so embarrassed to try, since it's normal there.  If really not interested, at least tried once, then can say not for them.

Those onsens in Hakone, with blackish minerals in the water (from the volcanic hotsprings), felt like floating in the sea. 

I think you're underestimating Tokyo a bit with this schedule - the first two days part. There's no way you can cover so many places in one day. Unless you're going for a 12 hour marathon everyday...

Nicely formatted itinerary ... I prefer this type ... no need to definitely go to certain place on certain day (unless it's a fixed date event) ... areas spread over few days, to give allowance for bad weather or bad moods  ... priority places first, KIV places if still got time.

That said, like what another mentioned, it's hard to cover those area in the first real 2 days ... let's say sprint + marathon:- Asakusa 2hrs (trying out foods like melon bun also, not just taking photos), Tokyo Skytree 2hrs (waiting + looking around time + shops; nvr went before, simply estimate), Ueno 4hrs (quite huge area... park, zoo if interested, museums...luckily not sakura season, else will be taking lots of photos), Akihabara 3hrs (depending on interest, if you ask me and my frens, 2 or 3 days also not enuf), Ginza 2hrs (again depending on whether windows shopping only or really shopping), Odaiba 5hrs (again, huuuge area ... so many places of interests here), Tsukiji outer market 2hrs (queuing to eat, windows shopping), and Toyosu 2hrs (dunno how long is the new tour, if still got guided tour for the tuna auction, last time in Tsukiji was only 15mins, waiting time I guess no need to wait like 2 or 3hrs previously) ...

Minimum total time already 22hrs ... maybe 11hrs per day, and that's rushing around, most probably can't really enjoy lor.  (Unless your goal is just to tick off places been to, or go there for a short while, and maybe see which area you'll go again for longer period in the future).

Well, if you want hassle free. Buy a new Digi Prepaid online, Rm8, reload the amount of credit base on how long you visit japan. Rm25 for 3 Days Roaming come with 2GB + 30mins voice call. 9 days visit in Japan just cost you Rm75.

Nope, No minimum credit balance needed. I topped Rm50 for 3 days + 3 days usage.