What do you mean by going to Narita? Stopover 1 night and not planning to go Tokyo? Or do you mean you will be in Tokyo but landing in Narita Airport? How many days? What activities and places do you plan to go to?

going with 5yo in tokyo?
u can try disney land (i will not recommend disneysea for ur 5yo unless u r fan of disneysea la, coz ur 1 week not really enough) , ueno zoo & akachan shopping (if u planning to have another baby, a lot baby stuff )
the rest is major famous tourist spot and shopping area which u can easily google and listed top10

Ghibli Museum will need advance booking. If you are in Japan you can buy it from lawson. IF not I think maybe Klook do sell it. As for accomodation, what is your budget. For some cheap can be 1000RM/day or 100/RM/day.

Ghibli Museum ticket, buy it online and get it at the original price of 1000yen per adult. Ticket sales for a particular month is available for sales on the 10th of previous month (e.g. tickets for October month will be released online on 10th September).

If not, prepare to pay higher price for it

nobody in their mind would get it from klook due to their price
it's almost double of the original pricing

hi bro , kkday don't have 

not only diaper. my formula baby milk also need to bring.
fuji 3 days are too much. lonely place there. better go Takayama shirakawago.

btw my 12 days for first timer.
please correct it if I miss something or my itinerary not full enough maybe recommend me other places to visit.

day 1
16.20 arrive Narita. took keisei bus 1000 yen. buy tokyo metro pass 3 days 1500 yen. sim card 500 yen
18.00 reach hotel stay at asakusa. 3 night 4500 yen
19.30 reach shiodome caretta illumination
20.00 eat gyudon matsuya 380 yen
22.00 arrived at asakusa hotel

total cost day 1: 7880 yen
day 2
08. 00 breakfast at matsuya 320 yen
09.00 sumida river
10.30 shinnobaizunaike temple
11.30 ueno park
12. 00 lunch matsuya 380 yen
17.30 dinner matsuya 380 yen
18.00 go sensoji temple
19.00 ji Ken bridge
21.00 back to hotel

total costs: 1080 yen
day 3

08.00 breakfast at matsuya 320 yen
09.00 nezu shrine
10.00 tokyo dome
11.00 meiji jingu
12.00 lunch matsuya 380 yen
12.30 takeshita street
13.00 meiji jingu gayen
14.00 the east garden imperial palace
15.00 meiji shrine
18.00 dinner matsuya 380 yen
19.00 reach hotel

total costs: 1080 yen

day 4

08.00 breakfast matsuya 320 yen
10.00 jenkokuji temple
11.00 arashimangu temple
12.00 lunch matsuya 380 yen
13.30 yoyogi park
15.00 tokyo metropolitan government
18.00 dinner matsuya 380 yen
19.00 shinjuku illumination
20.00 omoide yokocho
23.00 take bus kosoku to osaka 2300 yen

total costs: 3380 yen

day 5
airbnb 2000 yen for 3 nights. ( very cheap airbnb using referral code)
08.00 reach namba eat breakfast nakau 350 yen
11.00 explore dotonburi, kuromon ichiba
13.00 lunch matsuya 380 yen
15.00 check in hotel take rest whole day
18.00 dinner matsuya 380 yen

total costs: 3110 YEN
day 6
osaka amazing pass promo from klook 2800 yen
08.00 eat breakfast at nakau 350 yen
09.00 osaka castle
11.00 osaka jo gozabune boat
12.00 osaka museum house and living
13.00 eat matsuya 380 yen
14.00 go Legoland
17.00 glion museum
18.00 eat matsuya 380 yen
19.00 Nakano Shima river cruise
20.30 hep five ferris wheel
22.00 reach airbnb

total costs : 3910 yen

day 7
08.30 eat breakfast nakau 350 yen
09.30 tennoji zoo
11.00 red horse osaka wheel
12.00 eat matsuya 380 yen
13.00 tempozan giant wheel
14.30 tsutenkaku tower
16.30 eat matsuya 380 yen
17.30 umeda sky building
20.00 sakishima cosmo tower
22.00 reach airbnb

total cost: 1110 yen

Day 8
07.00 breakfast matsuya 320 yen
08.00 buy hankyu pass 1 day 800 yen
08.30 from namba to umeda 400 yen
11.00 kyoto bus pass 3 days 1800 yen
11.00 reach kyoto arashimaya
11.30 breakfast matsuya 380 yen
18.00 dinner matsuya 380 yen
19.00 reach hotel. 2 nights 4000 yen

total costs: 8080 yen

day 9
06.00 breakfast matsuya 320 yen
07.00 fushimi Inari tasha
12. 00 lunch matsuya 380 yen
12.30 higashimaya street
13.00 yasaka shrine maruyama park
14.00 chionin
15.00 heian
16.00 nanzenji
17.00 philosopher path
18.00 dinner matsuya 380 yen

total costs : 1080 yen

day 10
09.00 breakfast matsuya 320 yen
10.00 explore gion
13.00 lunch matsuya 380 yen
18.00 dinner matsuya 380 yen
22.00 kosoku bus 2500 yen to tokyo

total costs: 3580 yen

day 11
09. 00 breakfast matsuya 320 yen
09.30 tokyo metro pass 1 day 800 yen
10.00 nakamise shopping street
12.00 lunch matsuya 380 yen
14. 00 akibahara
18.00 dinner matsuya 380 yen
19.00 shibuya
22.00 arrive at hotel 1 night 1500 yen

total costs: 3380

day 12
09.00 breakfast matsuya 320 yen
11. 00 lunch at matsuya 380 yen
12.00 asakusa to Narita airport 1310 yen

total costs 2010 yen

total costs day 1-12: 39.680 yen

I prove that 3k ringgit is enough for 12 days.