Ahhhhh... It is nice to see a GOOD tech question one in a while. The misfire detection is actually not done the way you would think. One woud think that it is somehow monitored at the ignition level by monitoring the firing of the coils. It isn't though. It is monitored by calculations done on info sent from the crank sensor. The eec monitors the acceleration of the crankshaft wheel. It checks for deviations in the acceleration, and knows what cylinder should be firing at that time. A certain percentage of misfires are considered acceptable based on speed and load. If that threshold is exceeded first the time, the MIL should blink. If the misfire is detected again in the same driving cycle, the MIL will stay on. Misfires can cause raw fuel to go through the system and damage cats. To prevent this, if the eec continues to see misfires on a cylinder, it can disable that injector. Up to two injectors can be disabled.