The other day I was driving and started to notice a tap from the engine and car running rough. I got home and scanned it and have a p0300 and a p0306. The misfire counter on cylinder 6 is bad with residual misfires on cylinder 4 and 5 as well but not too bad. I have replaced the plugs, swapped coils and injectors, replaced fuel dampers, replaced valve cover gaskets as well as the lower and upper intake gaskets. I have ran a gas treatment through incase it was bad gas and also did an oil change with ester oil. Also have cleaned the mass airflow sensors and throttle bodies but I am still getting a bad misfire from cylinder 6 that even causes the CEL to flash. I am going to be doing a compression test on it this weekend to test that but does anyone else have any ideas what it may be? It's a 2012 G37x with 104k on it. Any help would be appreciated. Thank you.

 

Maybe bad harness

 

I have checked the harness all along the back of the motor and all the grounds and I dont see any damaged wires or wires chewed by any kind of rodents

 

I don’t know how our cars handled it but Honda’s would flash the CEL if it’s pre-igniting. Just something I thought of

 

A flashing CEL simply means a misfire, which you already know.

With all the work done so far, my next step would be to check the fuel pressure. Factory spec is ~51 psi.
Since this engine has a return-less fuel system you will need a fuel tap like this one:
https://cj-motorsports.com/products/fuel-tap-npt-2-bolt

and a 60-100 PSI gauge.

You also might want to have a look at your short/long term fuel trims in the free frame data. If you add the short term and the long term, the result should be between -15 to 15%.