I am 99% sure my long running limp mode issue is solved. Thanks to the guys at APR they pointed me in the right direction. After giving them the symptoms I've been having they insisted they knew what the problem was and told me to check the flap motor connector to make sure it is seated. So i check it and it looks connected (although the retention tab is missing) but i figured to make sure and give it a nudge and lo and behold the connector moved about 2 mm! It felt like the epiphany moment on House. The car went into limp mode under load is because the ECU still checks to see if the motor is there even if it isn't being used (flap delete kit) and when it saw that the motor was missing it went into limp mode. Which is why if i drove like a grandma the car was fine, because I never took it to the point the flap motor would have actuated. Been driving the car for 2 days now and still no issues. I still have a few other codes but they haven't affected drivability so I'll take my time with them. I am so unbelievably relieved because I was this close to taking it to a dealer which would have cost me a minimum of $310 for just the diag.
Codes: P2012, P2014, P0642 (for when people search)
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