I put together some tests for you to run so that we can pinpoint the problem.
The EGR flow on this vehicle leaves the valve and enters a large passage that runs through the lower intake manifold. From there it is fed to each individual cylinder through small orifices in each intake port. These orifices tend to become restricted with carbon, causing all EGR flow to enter the cylinders with no restriction creating a misfire on those cylinders. To test for this problem, simply unplug the vacuum hose from the EGR valve and road test. If the misfire is gone, remove the upper intake plenum and clean the passages in the lower intake manifold as needed
Tests/Procedures: 1. Disconnect the ignition coil and recheck for a flash on the test light on the PK/WH wire. If there is a good flash with the coil disconnected but not with it connected, suspect a shorted coil or a bad connection at the coil.
2. If there is no flash on the PK/WH wire with the coil disconnected either, access the Powertrain Control Module (PCM) connector behind the Right Front (RF) strut tower area.
3. Back probe pin 78 PK/WH wire and check for a trigger there with the test light still connected to battery positive and cranking the engine. If there is a good flash at the PCM connector but not at the coil, check the PK/WH wire for an open circuit between the two.
4. If there is no flash at the PCM connector, suspect a damaged PCM. Check for a shorted ignition coil before replacing the PCM. Also check the PK/WH wire for any continuity to ground or battery positive in the harness.
Potential Causes: Ignition Coil
Powertrain Control Module (PCM)
Tests/Procedures: 1. Start out with disconnecting the vacuum hose to the Exhaust Gas Recirculation Valve (EGR) and see if the problem is still there. If the problem is gone, clean out the EGR orifices, since clogged orifices will direct too much EGR flow to one or two cylinders. If the problem is still there, perform a manual power balance test while power braking to determine the cylinder that is misfiring.
2. Verify the cylinder in question has adequate spark. Use an inductive timing light on the cylinder in question. If the timing light stops flashing as the misfire occurs, the cylinder is losing spark.
3. If OK, check to see if the injector is losing injector pulse as the problem occurs. Monitor Long Fuel Trim (LFT) on the scan tool to see if it is abnormally high on the bank with the problematic cylinder which may indicate a restricted fuel injector.
4. If OK, perform a cranking and running compression test for mechanical problems.
Potential Causes: Engine - Base engine concerns.
Restricted Exhaust Gas Recirculation (EGR) Passages
Restricted Fuel Injector
Malfunctioning Secondary Ignition
Tech Tips: When performing an engine running compression test, remove the Schrader valve from the spark plug end of the compression tester hose so that the needle falls back to 0 PSI after each compression stroke. Disconnect and ground the spark plug wire. Start the engine and take an average of the peak of the reading on the cylinder. If necessary, connect a timing light to the plug wire so that a snap shot reading can be taken at the time of ignition. All cylinders tested should be within 10% of each other and the readings will typically be about 1/2 of that found from a cranking test.