Thanks for all of the input. Turns out it was the battery. Car is running fine now. Lesson learned, I will always have external power when flashing. I really apperciate this forum. I have learned alot just reading past threads.
The only thing that I unplugged was the mass air flow sensor so I could reinstall the reduction sleeve. I have read in a couple places that if I installed it backwards it cause similar issues. That will be the first thing I check when I get home.
I have a 2020 GT with the closed Roush CAI. Only other mods id the MBRP x pipe and Bama Rev X tuner. I just cleaned my air filter and reinstalled the reduction sleeve in the intake tube so I could flash the car back to the stock file. Once I did that I did not start the car to give filter time...