Not sure on this but thought that tax refund in normal stores is subject to a minimum purchase amount?

Does this mean if buy smaller amount, better to buy in duty free shop in airport, ie no need for tax refund or I understand it incorrectly?

you really should opt for private transfer, 470 one way is not expensive from narita to tokyo city, considering the kids and bags too. wont you want to relax also after 6-7 hours flight from KL as well? i suppose you will bring stroller too?

choose the alphards range..I booked mine last time via klook approx rm500.

You are right, thats why pre-booking helped "reduce" the cost.
I used their service 3 times so far. Nth negative, on time both drop to airport and pickup from airport.

Klook is only a platform for those vendors, but i doubt KLOOK will endorse nor promote any illegal operator in their bucket.
Albeit I cannot tell if is illegal in terms of local law or not but they are registered companies.