Hi hzrnbgy,
Thanks for your response!
Im working in the Hz range so there is about 6 orders of magnitude cushion between the signal frequency and the processor speed. The duty cycle for the PWM signal from the receiver ranges from 1 to 2ms and the frequency of the signal is 60hz.
To drive the stepper, I need an output signal of ~1.6kHz (fast speed) up to ~70 Hz (slow speed)(edited from original post) to the STEP pin (Im using a TMC2208). Duty cycle of the output signal doesnt matter as far as I know...because I think the stepper driver reads the rising edge of the signal to determine frequency. Keeping a constant 50% duty cycle seems to work fine.
Ill have to read into this timer stuff I guess there is no getting around it.