no one can tell, who know what will happen tomorrow
anyway, you are not exchange one million RM, the rate up & down won't effect you much

KL > Narita....no way. Too far way from Mt Fuji
Flight Path of ANA
https://www.flightradar24.com/data/flights/nh816#112a4f77

Flight Path of MAS
https://www.flightradar24.com/data/flights/mh70#1127b471

Flight Path of JAL
https://www.flightradar24.com/data/flights/jl724#11292fd2
Narita > KL ...Yes (Morning & Noon Flight Only) 
Flight Path of ANA
https://www.flightradar24.com/data/flights/nh815#11284e5c

Flight Path of MAS
https://www.flightradar24.com/MAS89/112a900e

If taking JAL from Narita to KuL then No Way......
Flight Path of JAL
https://www.flightradar24.com/JAL723/112aa65d
Conclusion....If want see Mt Fuji...Never take JAL.....  

With 2 years old kid but plan all until 12Am.....No way.....10pm Max he will sure fall in sleep due to fatigue.
Unless you going to carry him
If want go Hakone, can replace it on Day 3 because your Day 3 plan are not necessary.

Plus August was so Hot....34 - 37 Celcius.  By 12pm - 2pm you will be exhausted due to high heat, Resting at Hotel Room.
This also will ruin your plan, Alot thing need re-adjusted

then the following day need to start at 8am...gonna be difficult

most if not all of the days are ended quite late. Bare in mind Japanese store close usually at 8pm - 8.30pm so do plan ahead in case you are planning to go shopping.

Your Day 4 is too pack. By the time you finished Harajuku, either your kids or you will fell tired. Skip Shinjuku if you are not keen to shop. You can squueze in Hakone day trip if you think you can move all day 5 itinerary to day 1 to 3 night. But again, with kids are difficult.

I suggest you take out Ginza and go back your hotel to have an early rest. Will be too tired since you have a midnight flight and reach Tokyo early morning

Then on Day 2, you should go early to Tokyo Disneyland. Ideally half or 1 hr before the park opening times.

My comments below, the place you going similar my last trip.

Day 1 - Suggest drop Ginza have both dinner and fun playing with kids at Akihabara.
04:00PM – Ueno Ameya Yokocho Street
05:30PM – Akihabara – Electric Town
08.30PM – Ginza – Shopping district
11:00PM – Back to Hotel

Day 4 -  Thinking of going Meiji Shrine? Can visit there around 2.30pm then Harajuku 4.30pm time free to adjust.
11:30AM – Lunch - Nazebo Shabu2 - 6F Shibuya BEAM, 31-2 Udagawacho, Shibuya, Tokyo -1600Yen
04:30PM – Harajuku
• Takeshita dori street
• Meiji-jingumae 'Harajuku' Station - Meiji Shrine near Harajuku station
06:00PM – Tokyo Tower

Day5 - You may want to check the opening hours and last enter time for Metropolitan building. It also some walking distance from station your kids may be tired after Hakone day trip.
09:00AM – Hakone
05:00PM – Shinjuku
• Tokyo Metropolitan Building and explore shinjuku
• Dinner – Zauo fishing restaurant
10:30PM – Back to hotel

FYI, there is some construction going on around the shrine.
For me didn't much affected the whole experience but the entrance u will see construction and some parts are closed

https://www.japan-guide.com/e/e3002.html

Those 3 lines you've listed are run by JR. There are trains covered by the toei subway/tokyo metro pass from Asakusa to Shinjuku but you will need to change lines at certain station(s).

Tokyo Metro Pass can used on Tokyo [[ONLY]] JR Line.
BTW, Tokyo Metro Pass are very expensive, unless you taking alot alot train per day...if not using Suica / Pasmo more convenience

You gotta do your homework more in depth to find. It is not hard to find if the station you wish to go on is being covered by Metro or any other train services.

From Shimbashi Station to Tokyo Teleport Station via Yurikamome Line is covered by Metro Pass, if you wish to use PASMO/SUICA is JPY320.

Tobu Skytree Line

You will need to check the opening hours of stores and shrines. They're not like Malaysia, open till late.

Day 1 - Ginza Uniqlo, GU etc closes at 9pm, for your info.
Day 2 - After Disneyland, I'm not sure you'll still have energy left to shop at Don Quijote. But anyway you can try, coz it's 24 hours.
Day 3 - You can actually board the water bus from Asakusa all the way to Odaiba. Very pleasant ride, just to share.
Day 4 - Hate to break this to you but Meiji Shrine closes at 6pm; however around 5.30pm they will start to announce. And it's a long walk from the front tori to the shrine itself. Easily 15-20min depending on your pace. Don't forget you'll have to allocate the time to walk back to the entrance to leave the shrine.
Harajuku starts closing around 7-8pm.

P/S: FINALLY HOME!!! Had a pleasant trip but also a fair share of misfortunes; some of you in the chat group and my FB will know. I'll share it again on a separate post here.

what time you're landing? I think day 1 not enough time if you wanna land then go check in then go for the romantic train like that
for day 5 you have any particular place you wanna visit? I would suggest day 5 to put only Hakone so that you don't have to rush. you can put shinjuku into day 4. shinjuku and shibuya are like neighbour city

Looked good at the moment and it's more do-able than previous itinerary. I knew my group (and me too) was too greedy previously that our itinerary was pretty packed everyday. While we managed to do most of them, every morning it's hell trying to get up. Most people will understand this on... the 3rd day onwards hahahaha.

Just some additional comments/ pointers:
- Asakusa is really huge, but you'll see shops starting to open from 10.30 to 11am onwards. So even if you leave accommodation early, there's nothing to see yet.

- On Day 3, just take note that Tsukiji starts to close around noon or 1pm, so be sure to arrive early.

- In Odaiba, there are few things to do/ see: visit Fuji TV exhibit, chibi maruko cafe, Diver City's Gundam (check the performance time) and Decks (to see rainbow bridge, statue of liberty etc). So in my opinion, Odaiba is beautiful at night - both the Gundam and night view breath taking.

- Day 4, yes do Meiji >> Takeshita Dori. You can also buy bento/ sandwiches etc and eat in Yoyogi Park. Yoyogi Park is just next to Meiji Shrine. If you don't want to make the detour, then I suggest before going to Meiji purchase your lunch meals. After Meiji, straightaway head to Yoyogi and have a relaxing/ fun picnic. Then get to Takeshita Dori and have the Harajuku Crepes, Zaku Zaku ice cream etc

- Get your Hakone pass earlier and not on the day you're going. Buy in advance and I suggest to top up for Romancecar; it helps you get there faster and earlier. Ask the Odakyu counter about Romance car: https://www.odakyu.jp/english/romancecar/

- Lastly, everyday before leaving the hotel/ house, check the weather forecast. If there will be rain, prepare/ buy an umbrella beforehand. It helps a lot to prepare in advance.

No problem on the water bus, just a recommendation. At least you manage to do 1 way! I will assume you're staying in Asakusa throughout your trip? Wise choice from Asakusa station, you can get to airport directly (be it Haneda or Narita) without any transit.

However the less-desirable part of it would be: staircase only. It's a pretty long way going down and then up some stairs in that station. There's no escalator nor lift.

Would love to recommend onsen if you could make time but unfortunately it already seemed pack and Hakone is only day trip. No worries, you'll find it slightly easier to plan the next time onwards All the best and have fun!
I think he probably meant Day 5's night time to visit Shinjuku's Kabukicho. I think by 5 or 6pm, the bus from Hakone to the station is getting lesser. As such, they will have no choice but to leave around that time. Likely to arrive back Shinjuku around 8+ latest. In that case, there's still time to visit Kabukicho for around 1-2 hours and have dinner there.

Besides, Kabukicho gets better the later it is

you didn't mention the airline that you have booked ...
14 - 15 days for 4 main cities...?

do you mean travelling period is Nov 2018 or...?