One more thing to add about the seal - when you place the cover back on you have to torque (8.7 lbs for cover bolts) them evenly as mentioned above, but also have to do it in a certain sequence (can't remember sequence exactly, but remember seeing the sequence pattern under the autozone website when I was looking up the manifold system). I would say go buy a new seal, properly torque it back on at recommended settings and sequence.
I have a question for OP - I understand how you cleaned the cover, but how did you clean the ports without having debris fall back down and make things worse?
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