Duke
To run one motor at a time you can change the motor control from PWM to CAN on the motors you don't want to run.
Your vibrations is what caused the graph of your motor PWM values to look like you have a lot of motor clipping. Once your vibration are under control everything will be good.
I think the crash caused the vibration problems because you have been able to fly well before the crash with your old AQ board..
Larry