1997 Grand Am Ignition Problems

I have a 1997 Pontiac Grand Am (2.4L) that is missing fire on the number 1 and 3 cylinders. I have replaced the spark plugs, the plug boots, the coil pack housing, the coils, the Ignition Control Module, and the Crankshaft Positioning Sensor. Additionally, I have replaced the fuel filter, removed the fuel rail and visually checked that the fuel injectors were firing (they were). I have run out of ideas as to why these two cylinders are not firing. Any assistance would be greatly appreciated.

Welcome to AF !

When you say "missing fire" do you mean it's showing a trouble code for a misfire?

If so whats the exact code ??

I receive a P0300 code for a misfire. While looking at the computer screen, you can see that the number 1 cylinder has a high number of misfires (100-200) while the number 3 ccylinder has a few misfires (3-80) each cycle. This is the only trouble code that the computer is displaying. After installing the new crankshaft positioning sensor, I tried to re-learn the sensor, however, I cannot get the engine up the required rpm (over 3900) for the computer to complete the learning process.

Since you have repalced all the ignition components I would test the injectors, especialy the one with the excess misfires.

Measure the resisteance acrossed the injector(s) terminals. Your 4 cylinder should be 1.95-2.3 Ohms.
You can rent/buy a Noid light to test if the signal is coming from the PCM correctly.

If either of those tests fail I would replace that injector.