Personally i feel easier to find cheap food in Japan compared to Seoul.

In Japan 1 meal cost around 500-1000 yen which translate about 40 MYR now. 1k yen food is quite good already. Most of the time I'm having those 600 yen food. In South Korea I heard 1 meal averagely cost about 35-50 MYR.

As for the products, I am not sure which place is cheaper.

hi guy, do you think below schedule is ok?

Day1
-Noryangjin fish market
-Itaewon
-Dongdaemun
-Gwangjang Market
-Cheonggyecheob stream
Day2
-Coex Mall + Aquarium
-Gangnam
-Shinsa-dong
-Sinchon
-Ewha
-Hongdae

Day3
-Gyeongbokung
-Gwanghwamun -> Cheonggyecheon
-Tosokchun
-Bukchon Hanok village
-Insadong

Day4
-Namdaemun
-Myeongdong
-Namsan Park
-N seoul tower

Day5
-Everland

Day6
-Namisan Island
-Petite France
-Lotte Mart

hi yvonne, i have re-arrange my schedule,

Please kind advise

Day1
-Dongdaemun
-Gwangjang Market

Day2
-Noryangjin fish market
-Coex Mall + Aquarium
-Gangnam
-Shinsa-dong
-Sinchon
-Ewha
-Hongdae
-lotte tower

Day3
-Gwanghwamun
-Cheongye stream
-Gyeongbokung
-Tosokchun
-Bukchon Hanok village
-Insadong
Day4
-Namdaemun
-Myeongdong
-Namsan Park
-N seoul tower
-Itaewon

Day5
-Everland

Day6
-Namisan Island
-Petite France
-Lotte Mart

because i will be staying in dongdaemun,so first day probably will go some where nearby.

Some small comments;

Day 2 is freaking packed, if you're gonna go from Hongdae to Lotte Tower which I'm pretty sure would already be late evening if not night time, then there is almost no point in going to Hongdae in the first place. Hongdae comes to life at night, not in the afternoon. Suggest to just skip Lotte World all together, nothing special about the observation deck to be very frank with you.

I suggest spending your time in Hongdae instead, lots of things to eat, do, and party. If you want, you can even go to a Nanta show.

Gyeongbokgung is cool and all, but it's the more popular palace and thus it's also the one with the most generalization for foreigners. Changdeokgung on the other hand is a lot more true to itself and the secret garden at this time is just BEAUTIFUL! But since you are going to the Hanok village, I guess Gyeongbokgung is the more logical palace to visit.
As a person who resided and worked in S.Korea for a few years before, yes this is a real thing.
However, it's not as widespread as that article is trying to claim. Just like you've never encountered such thing in Taiwan, can you say that it isn't happening in Taiwan?

The foreigner menu thing, that's given to foreigners because they THINK that you won't be able to eat their spicy food or in some cases - some "ahem" meats like; horse, dog, or whatever in the more extreme cases. Sometimes they are priced differently because well... the ingredients that goes into the "foreigner" menu is different too. If not sure, just ask. If don't know how to ask, then too bad - learn how to ask.

I personally has never, ever (not even once in my 3 years at S.Korea) been given a foreigner menu though, not even in foreigner infested areas like Myeongdong.
As for transport, lol if you take subway how the heck is the subway going to cheat you? If you mean taxi drivers, they always use the meter BUT their meter is counted based on how far the distance from point A to B is.
There are obviously drivers who would take a long route, but at the same time how are they going to earn if the passenger wants to go from say Gyeongbokgung palce to Changdeokgung palace? The route is like 5 minutes tops (with moderate traffic), the petrol used to get there would cost nearly as much. So how? Charge 2000 yen and call it a day?

As for clothes, pandai pandai lah. Who ask to buy at flea markets when you know they were all imported directly from China anyways. Same thing in Malaysia what.
Finally, what makes you think tour agencies aren't scamming their customers either? I look at their itineraries and I know some of the places aren't even tourist worthy, many of them are questionable. But let ignorance be bliss right?