Cylinder-specific misfires are pretty easily determined by a combination of the consistency of the crank position sensor signal pulses and monitoring the resistance/voltage through the coils. Tiny variations of the speed of the crank through it's rotation make it easy for the ECU to determine whether any specific cylinder is firing or not. The ECU also monitors coil voltage, which relates to resistance across the spark gap. Low resistance, cylinder is firing. High resistance, not firing = misfire. Easy peasy.
