It's the tune. Even if the rear o2's were kept on in your tune you'll still have trouble passing with an aftermarket tune. If you were to revert back to the stock tune the monitors would reset pretty quickly. I was in the same boat with my 2011 GT. Could not get the car to pass so I put it back...
Ted knows a lot about the newer Camaros but is clueless on the newer Mustangs say 2011 to present time. Plus he overcharges for his work and parts. And God forbid you let him tune your car...........
The 3.73's are going to be detrimental as they'll more than likely force a shift into 4th gear dropping you out of your powerband. I would go with a shorter tire but something is definitely not right. My 60' was 1.5 with a 4C converter and 3.15's.