My buddy who also has a DPI exhaust came over and listened and said his car makes the same noise. He said his friend who has a new Mustang had the same thing and they told him at the Ford dealership that it was just something that happened with that kind of exhaust. I did find a few loose nuts on the exhaust manifold if that has anything to do with anything. Wondering if this is another case of simultaneous but unrelated issues...

(Also, the car passed emissions, would it if it actually had a misfire?)