While I wait for my friend to bring my OBD-II scanner back to me this afternoon I figured I should make a post to see if anyone has any ideas on what this may be. I hear this random thud / pop sound when the car is running. I've driven it around and gotten it up to temperature and filled it with gas, but in both cases the issue persists.

 

To me in sounds like a flap or something not holding. There is a flap on the air intake box that opens into a resonator. When driving, does the intake sound change pitch each time it pops? When working on my car a while back, I removed the air intake and the flap was broken. When I propped it open and closed it by hand, it sounded very similar.

 

Doesn’t really change no. I checked misfires and there were 36 after a 20 minute drive so I’m thinking either spark plugs (which are due) or cleaning the throttle body which hasn’t been done.

 

That makes sense. Did all 36 misfires occur during the previous drive? On my scanner, the misfire count is for the last ten starts.

 

I believe they're from each start as I've seen the numbers go down when I did a few drives to test around. Car is awaiting service now but David Modderman seemed to back what was suggested to me by Alex at Sharkwerks: plugs, coils, clean throttle body first. My biggest concern is that it's bore scoring, even though I know that's logically not common in the DFI engines and the misfire count is incredibly low at the moment (less than 1 misfire per minute).