Just running the reflash is going to run super rich till you tune it so that may be why your getting all these codes. If the car was running fine with the stock calibration I would leave that till your get a proper tune. I would wait for a DP if you don't have one to start tuning. Also if your running a 3.5" intake with no tune be mindful of possible damage to your catalytic converter from excessive fuel burning due to MAF readings being skewed. Not sure the reflash is specific for just intake mods or intake/dp or just dp or whatever combo your running. It's made to just have your car run till you get it tuned properly. I did a test with my PRL Short ram and this is what I saw through my obd scanner.
I threw on my PRL short ram the other night with no FP just for a visual and curiosity on sound and NO I did not keep it on or run it long. Sounds mean and looks great but I plugged in my scan tool to read the PID data as I ran the car so I could understand how bad the car actually ran. Yea don't ever run a 3.5" with no tune if you care for your car. Fuel trims almost 50% rich and my cat went from 400 to 1200F in just over a minute burning all the extra fuel. You WILL cause damage with no tune. Just thought I'd share that