The way the pcm reads misfires is based on info from the crank sensor (to know which cylinder) and the knock sensors detecting something being off. Say for example if your compression is low, that could give you a misfire code.
While you are working on it, if you checked say cylinder 3 compression and it comes up as 180ish, that would point you to maybe a chipped piston or something keeping you from getting good combustion in #1.
Is this an NA or SC engine?