If 3 was noticably darker than 1 then it suggests a problem with 3. It looked a bit dark to me, but hard to tell from photo.
Its possible that its either not firing spark plug correctly or the 3 injector is leaky/defective and its running rich on that cylinder as a result
you done coil and plug, so swapping 1/3 injectors and see if misfire starts on 1.
Its then possible its leaky damaged direct injector, but thats a crap load of work and expense and you would not want to do that without proper diagnosis. They are matched set and all seals and fuel rails should be replaced if removed.
alter that its looking difficult like weird wiring fault
looks like shop time
http://www.ft86club.com/files/BRZwiringi.pdf