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My check engine light came on and the engine started running rough, so I changed the spark plugs. Still running rough. Code says cylinder 3 misfire, so I disconnected coil and the level of roughness didn't change. Switched coils with another cylinder to confirm problem was the coil, but nothing changed. So the problem isn't spark plugs or coils. I'm thinking perhaps it's the powertrain control module, so I want to first reset it to see if that fixes the problem. But I don't know where it is. Can someone help me? Any advice of what the problem could also be?
 

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How many miles on your ride ? I also experienced these things on my 06 .. if you have high mileage when was the last time you did a valve adjustment?

Welcome to the Forums btw !
 
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Hmm, I would start with easily replaced parts first (if they have not been replaced yet). EGR, PCV, engine air filter. Changing the spark plugs a little early also helps. Thanks.
 

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My check engine light came on and the engine started running rough, so I changed the spark plugs. Still running rough. Code says cylinder 3 misfire, so I disconnected coil and the level of roughness didn't change. Switched coils with another cylinder to confirm problem was the coil, but nothing changed. So the problem isn't spark plugs or coils. I'm thinking perhaps it's the powertrain control module, so I want to first reset it to see if that fixes the problem. But I don't know where it is. Can someone help me? Any advice of what the problem could also be?
With high miles, the EGR passages often become clogged with soot, and can cause misfires. If it gets bad enough, the VTM 4 system on AWD models will be turned off, and the VTM 4 light will go on along with the check engine light.

To check this out and clean the passages, remove the inspection plate on top center of the intake manifold. underneath you should see the passages and small access ports for each cylinder. Use a shop vac and small scrapers, probes, brushes to remove the carbon. If you have over 150k miles, this is a common issue.

New PCV valve is probably also needed. How dirty is the air filter?

The engine computer is pretty robust, and I would be surprised if that is your problem.
 
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