Remove TIM2 CH1 CH2 PWM configuration
Enable TIM2 CH1 CH2 input capture mode

TIM2 CH1 is PWM3, TIM2 CH2 is PWM4.
Pin Config:
https://github.com/Hom19910422/QCopterFlightControl/wiki/Config
Remove TIM2 CH3 CH4 PWM Config

Because we still have TIM CH3 and CH4 in PWM config, It has some  time
base conflic problem. I decide I will not use TIM for PWM output in
future.
Rearrange initial configuration
Enable TIM2 CH1 and CH2 to capture PWM pulse