Hyundai Repair: Sonata 2001 ignition problems, powertrain control module pcm, powertrain control module

Question
I am in Canada.  I have a 2001 Sonata 2.4 that has been losing ignition to 2 of the cylinders. One coil fails after about 10 minutes and the car stalls and will not start again.  The next morning , it will start and run fine for the same time, then the coil fails again and the car dies. I changed the coil but it did not fix the problem. I have checked crank and cam sensors and they are fine. I don't believe they are the problem either. There is a small module on the back side of the head - it has four pins. I was told it was called an ignition failure module and I believe it is an amplifier for the crank sensor to fire the coil and is that true -- can it kill the fire on one coil and not the other.  Could this be the problem? - I have hit a wall on this.

Answer
The following presumes that the you're not getting spark out of only one of the coils as you indicate.  If you only know that the cylinders aren't firing but haven't verified there is no spark the coil, then you should begin with that diagnostic procedure first.  Similarly, if both coils are not applying spark, then the following won't apply.

Although the ignition failure sensor provides power to the coil and monitors the power and ground for the coils, it doesn't control the actual firing of the coils and is in no way related to the crank sensor.  Additionally, because of the way it's wired, it cannot affect just one coil, so we can dismiss the ignition failure sensor as a possible cause.  It's more likely that you have a poor connection at one of the coils, a problem with your powertrain control module (PCM), or a problem with the ignition control wire running between the coil in question and the PCM.  

A good first step is to swap your coils.  This will verify whether the problem is with the coil.  If the problem moves with the coil, then there's a problem with the coil itself.  Since the coil is new and is having exactly the same problem as the old coil, I'd suspect that this problem is caused by the PCM leaving the coil on too long, causing it to overheat.  This is very rare, but I have seen it once and heard of a few other instances.

If the problem stays on the same cylinders, then you know for certain that the issue is with the connector, the wiring, or the PCM.