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I would replace the #3 coil, at the very least swap it for the one next to it and see if the misfire moves to that cylinder. It's possible there is something more going on, but typically the coils wear out and start to misfire. Swap #3 and see if it moves.
Also, sometimes when you replace the plugs it can disturb the coils and cause multiple misfires, but I suspect the computer just can't determine it's #3 because the new plugs are working so well.
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