TLDR: After replacing hardware and reflashing back to stock your car wont be immediately ready to smog. You'll need to drive around normally for a week or so to ensure all your sensors are re-activated.
I switched back to stock hardware and reflashed to the OEM tune. Drove out for 20 or so miles and then took the car to the smog shop. The pre-check showed the Oxygen Sensor, Catalytic Converter sensor, and Evap system were not yet active.
At the shop's recommendation, I took a drive out for 100 or so miles up in the hills. Upon my return, the O2 and Cat sensors had activated and were showing green, but the Evap sensor was not yet active. The shop said to let the car cool completely and before starting the next day, open up the fuel cap for 10 seconds and then close, before starting the car. Apparently this helps reset the Evap sensor. Otherwise, all I have to do is drive the car for about a week before the final sensor is good to go.