Do you mean you move the cart by main or by code? IMO high pendulum speed does not occur with high cart speed, as long as the system remains stable.
Some questions:
- How do you control the cart?
- What are your touch sensors? Left/right track limit or touch pad for input? Light barriers instead don't need debouncing.
- Why do you care so much about pulses in code, when angle and position (value and/or speed) are sufficient for control?
- Are you sure that serial communication does not block your code? High pulse rate will force high communication rate, at the wrong time.