[pdbrains]

The coil is really two coils in one package. This means that the "coil" is always firing two cylinders at the same time. So coil 1 fires cylinders 1 and 4 and coil 2 fires cylinders 2 and 3. One cylinder on the compression stroke and the other is on the exhaust stroke and is wasted. You need to check if the coil that is missing spark is getting its 12 volts on the primary side and being grounded on the PCM side. The ASD relay provides this voltage to the primary side of each coil not the PCM. The PCM grounds the other side of the coil primary side and then "opens" it at the proper time to create the spark. Since it appears that one side is working you can compare whats happening on the primary side of the working coil with the non-working coil. You may be able to see the switching or not switching with a voltmeter when the engine is cranked, but you really need an oscilloscope. This is a very easy test and the dealer should have done this before the PCM was replaced.

So I suggest you take a look at whats happening at pins 1 and 3 of the coil connector. Pin 2 should be steady 12vdc. Pins 1 and 3 should be switching when the engine is cranked or is running. Good luck.