Just focusing on tokyo? maybe a day trip to hakone or nikko?

There's no one size fits all itinerary. You make plans based on what your interests are.

Day 3 -Tsukiji Market is relocating in Nov 2016. Will you make it before then? After Nov, it'll be at Toyasu/Odaiba. On a nice clear day, Tokyo Tower offers clear views as far as Mt Fuji. You can consider visiting Tokyo Tower at night or after sundown.

Day 7 - Roppongi is not really a must visit place unless you are specifically after clubbing or Hard Rock Cafe experience. I'd try to plan visiting Shibuya in the morning and spending the rest of the day at Shimokitazawa as it is nearer. Get to Shimokitazawa before dark to find your way around as the train station is undergoing extensive renovation.

Day 9 - I'll scrap Disneyland and head over to Yokohama. This will allow you to compare and contrast both cities. It's very near and suitable for a day trip. There's a Nissin Cup Noodle Museum, Kirin Beer Factory (free 45 min tours and 3 free drinks at the end of the tour) and lots of other stuff to see.

Plan light on your last day, especially if weather is bad, in order to allow you sufficient time to get to Narita Airport. In severe weather (overnight or extensive raining), services of express trains like Narita Express can be disrupted.

You might want to try a love hotel or a capsule hotel at Shibuya just for a night if that's the case.

If you're staying at Asakusa/Ueno, Yokohama is an hour away nia. Avoid the Chinatown in Yokohama and you stunt be disappointed.

Bandai Museum. Interesting... 

I am travelling to Japan this november. It is 7D7N since i will arrive in Tokyo late at night. I am plan to spend 3N in Tokyo 1N in hakone and 2@3N at Osaka. Need advice on JR pass since it is around MYR1060 for 7days validity. Worth it or not?

I rather sleep at Haneda Airport.
Lepak outside at midnight until first train will be very cold. With luggage summore, not convenient.
Shibuya Mark City open at 10am to 11pm only.
It won't be nice siting at Cerulean Tower Tokyu Hotel Lobby until morning plus you are not staying in this hotel. On Moral side it should't be done. Don't be like those China rude tourist.

Sitting inside Bus crossing Tokyo bay Aqua have nothing to see. Feel like crossing Penang Bridge only. Plus half way will go under Sea tunnel then nothing to see already.

I had tried stay overnight but trust me it is not worth it. Dont spoil your first day suffering without sleep wondering in airport. Pay for the hotel. You can still get to city via metro or bus.

i suggest u better sleepover @haneda airport
http://www.sleepinginairports.net/asia/tokyo_haneda.htm
there hv restaurant/charging area/free wifi
u dont wan to lepak at outdoor/cold place, and the trouble with police for loitering
disclaimer: never sleepover at haneda b4

also next morning @haneda, u can buy the metro pass/data sims/pocket wifi etc

you can use the coin locker in Shinjuku station (i assume you depart to Kawaguchiko from there)

if you are staying at a hotel after you return from Kawaguchiko, you can also ask them to keep your luggage first.

u know that place is not halal rite?

i been there, highly recommended... for food or strolling... either one of them is goooding
the walkway is very narrow, not for u to loitering,
in the nite itself... it is really cold
go check some of the youtube video 

anyway i aldy voice my opinions, u decide yourself