I have a similar situation. My 2017 mustang gt , 6 spd has 2 incompletes that will not clear. In 2019 I installed Borla ATAK, 2 1/2 in. exhaust and Airaid cold air, The car passed inspection the following month, Six months later I was clearing cob webs, missed a shift (****** shifter). Drove a mile and CHECK ENGINE. Took to realspeed he did nothing, except scratch my car and take my money. The manifold flaps broke. Installed a 2018 manifold that flows one more liter of air. With a tune from VMP, still won't pass!!!!! Multiple tunes etc, still 2 incomplete, which are EVAP AND FUEL. The car was fine until the manifold broke, so after all this, Another 2017 manifold and leave the rest as is, see what happens if it will complete. That was the short version. Drove it 2000 miles plus, goes like hell too! Does that help or can you help me?