KTuner.com

The first time I flashed my ECU I had no issues. Then reflashed my ECU and ended up going into recovery a few times but eventually was successful. I figured the ECU was back to stock. The battery was also dead so I charged it up a while. After starting it up I noticed a few warning lights (Brake, Tire pressure, Traction control, ABS) So I shut it off and flashed it to factory. After starting it up I noticed none of the lights went away and the steering light was on and a slightly rough idle that wasn't there before.

Ktuner module says there are no codes. Is it possible I just need to drive it to restart the systems?

KTuner only shows you error codes in the ECU, as that's the only module we flash. if your unit is up to date on firmware then clearing codes does issue a clear command for all modules.