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There are conflicting answers on this website, as the rules have changed.
Currently, however, as stated by Timatic:
Visa required, except for passengers with a visa issued by Australia, Canada, New Zealand or USA [...] holding confirmed onward tickets on flights departing within 30 days
and
Visa required, except for Holders of onward tickets transiting Seoul Incheon (ICN), participating in the Transit Tourism Program for a max. transit time of 72 hours. Leaving the transit area is permitted, provided staying in Seoul, Incheon or Gyeonggi Province. Leaving the tour group is not permitted.
As such, Japanese residency does not enable you to transit by yourself under the 30-day provision. In addition:
Visa required, except for Holders of onward tickets transiting Seoul Incheon (ICN), for a max. transit time of 24 hours.
In other words, you have two options:
Booking a Transit Tourism Program group tour
Obtaining a transit visa
Because your transit time is more than 24 hours, the airline will deny you boarding without a Korean transit visa unless you can show you've booked a Transit Tourism Program group tour