This is an interesting topic. I've been following East Asian politics for a while. While I agree with the OP on some points, the OP sounds quite biased in that s/he is depicting the Korean political context or views in a cartoonish manner while faithfully reiterating official Japanese claims on all fronts.
The OP basically insinuated that Koreans are simple-minded people who can just say "The Japanese are bad people" when they hear "Japan", which itself is a very simplistic and twisted view of the vibrant democratic society. If interested, one can take a look at nuanced in-depth surveys that the
Genron NPO has conducted. Click the link for full reports.
South Korean officials are of course trying to deny this and are saying that this is Japanese retaliation for the decisions made by South Korean courts to force Japanese companies to provide compensation for forced labour in WWII (A court decision that goes against the agreements of 1965 and 2015). However SK officials have been caught on record admitting that around 160 units of these materials are unaccounted for.
Where did you get that part? In most articles I've read, the 'security concern' raised by Tokyo was brushed off as a mere facade to sidestep trouble because as a WTO member, you are not supposed to weaponize trade for political reasons apart from national security concerns. Tokyo would be foolish to openly admit they are retaliating against the Korean court's decisions.
[Washington Post] Japan claims it's restricting exports to South Korea because of 'national security'. Here's the real reason why.
[New York Times] Japan cites 'national security' in free trade crackdown. Sound Familiar?
[Diplomat] What's driving Japan's trade restrictions on South Korea?
[Foreign Policy] Why are Japan and South Korea in a trade fight?
I don't understand why they were on the white list to begin with, If Singapore and Taiwan + the majority of ASEAN countries aren't on it what makes SK officials think they deserve special treatment.
I'm not sure why Singapore is not on the list, either. As for South Korea, they are the third biggest importer of Japanese goods. There must have been economic and/or political incentives for Tokyo to bring South Korea into the club in 2004.
List of the largest trading partners of Japan (2017)
I'm running out of time. I will revisit this thread later.