Stubborn Misfire codes (P0316)

[Driv3n to Dr1ve]

So I’m trying to resolve a multiple misfire code. Car is a 2015 GT tuned with a 350 manifold, PMAS 120 mm, kooks long tubes. I’ve swapped plugs to new motorcraft oem, done crank relearns, and the code is still present.
What else could cause a misfire? Other than the code, the car runs fine. I just want to ensure this isn’t indicative of a larger issue.

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[MiamiGT350]

Are the codes random or at specific gear/rpm?

 

[Driv3n to Dr1ve]

Are the codes random or at specific gear/rpm?

The P0316 is at startup, so it doesn’t occur while I’m driving. Also I have a CEL anyways for my cats so I can’t tell if it pops up anytime while driving.

 

[WildHorse]

9:1 odds it's the tune and you just didn't notice.

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