You may have broken/damaged a spark plug wire when pulling the wires off the spark plugs.
Use the cylinder balance test below to find any bad cylinders or sensor problems.
Cylinder balance test: use this to find dead or weak cylinders:
Revised 25 March 2012 to add necessity allowing the KOEO tests to finish before starting the engine and the need for a properly functioning IAB/IAC to run the cylinder balance test.
The computer has a cylinder balance test that helps locate cylinders with low power output. You’ll need to dump the codes out of the computer and make sure that you have the A/C off, clutch depressed to the floor and the transmission in neutral. Fail to do this and you can’t do the engine running dump codes test that allows you to do the cylinder balance test.
The OBDII should also have a cylinder balance test. Getting to it on the OBDII scanner will require some tinkering and thought. It seems that every OBDII scanner has a different menu path to get to options.Unfortunately, most of this very helpful info does not apply in this case - he's got a V6, not a V8. The diagnostic port under the dash in the driver's footwell is active and functional on the OBD-II V6. However, your idea is sound - one of the spark plug wires could be damaged.
JTipp, did you gap the new spark plugs? If the gap varies too much between the spark plugs, it could cause the engine to run rough.
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