I've done that before. Obviously when I load the stock tune, It sets the MIL light for O2 Sensors and Heater. They are there and working, but the Long Tubes and Catback set it off.
What codes do you get exactly, when you load the stock tune back on? The longtubes and catback shouldn't have anything to do with a MIL, but I could see it throwing a code for the downstream O2 sensors if you have no cats, or if the downstream O2 sensors are somehow turned off in the tune. Knowing the codes with the stock tune is really the key here to finding a solution to the issues you're experiencing. You may have a hard fault of some sort, which the tune is changing parameters and ignoring a fault condition.