Electronic – stack two l293d h-bridge IC’s to drive more current

It's because of the amount of current you need to drive the motor, the arduino can't supply much.

1) 31KHz is a much more reasonable PWM frequency than 500Hz. Motors will act like a low-pass-filter and generally give you the DC equivalent of your PWM but with very low frequency PWM that gets dicey - as you've seen. In general, you should increase the frequency of the PWM above the bandwidth of the motor - otherwise it sees a square wave rather than a DC voltage. 31KHz is right in the range of most motor controllers I've seen. You generally want it high but not too high (HF noise may couple into other parts of the circuit, etc.). It looks like you're in a good range with 31KHz.

2) It shouldn't affect those bit rates. The peripherals ought to have their own dividers and scalers and should be driven off of the main clock and not a peripheral timer. I can't speak to the pulseIn function though.