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Thanks man I appreciate it!Only seen that P0641 code one time before. And it turned out to be the harness that runs along the driver's side dog bone mount rubbed through. But here is what I found on it.
P0641 5-Volt Reference 1 Circuit Malfunction - With Automatic Transmission
Possible Causes Setting Conditions
• 5v VREF circuit to one of the sensors is open
• 5v VREF circuit to one of the sensors is shorted to ground or to voltage
• EGR, FTP or MAP sensor has failed
• PCM has failed
Key on or engine running and the PCM detected the 5-volt Reference 1 voltage was out-of-tolerance for 0.5 second. This reference circuit provides power to the Exhaust Gas Recirculation (EGR), Fuel Tank Pressure (FTP) and the Manifold Air Pressure (MAP) sensor.
It looks like the gray wire is the 5 VT reference wire. Hopefully it is just a shorted sensor, but it may be a wire that rubbed through.
As for the misfire on #3, it could be a bad coil or injector, since you have already swapped plugs and wires.
hope this helps