I had the same problem about 7,000 miles after I replaced the spark plugs, wires and coil pack. It was driving me crazy. I replaced a lot of other stuff trying to solve the problem. I did not check the spark plugs because they were so new.
I finally gave in and took it to a dealer for diagnostics. They found #3 cylinder had a slight misfire. The spark plug was tracking (arcing along side the ceramic insulator to the base). They replaced it and the car runs perfect now.
I inspected the spark plug and could see the arc marks. I thought the plug was defective and sent it back to Autolite. They determined there was no defect in the plug.
My conclusion is that when I installed it something like lint or hair got in between the spark plug and the boot. Over the 7,000 miles it slowly turned to carbon and began arcing enough to cause a slight misfire.
It may not be you plugs but it sure would be a good idea to pull them and check for any evidence of tracking. I wish I would have, it would have saved me $100.
Another thing that can cause this kind of misfire is the DPFE or EGR sensor. I thought for sure it would solve my problem when I replaced it. It did seem to get better but not totally fixed.
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