The PCM can determine if a particular cylinder is having issues, but how?

How does it know its cyl 1 and not cyl 3?

 

In simplest form there is a crank and a cam position sensors, between the two the PCM can determine which piston and stoke.

It is not a perfect circuit and is known to be flawed even by EPA which required the misfire watchdog to protect the cats.
The crank sensor looks for any change in crank rotation and assumes it is misfire but other things can cause crank change such as a warped rotor, ABS, and even a crank pulley that is not
properly balanced, esp undersized ones which will trigger misfire counters.

 

John is right, but pcm looks at velocity changes in piston travel which it measures with cam/crank sensors, any uneven loading from drivetrain can disturb crank speed but pcm has allowances for slight momentary changes in crank inertia.

 

Wow. I didn't realize it was that complex.

Thanks for the info.