I see. I was wondering for a moment if the ADC would be able to keep up, but it seems it's capable of sample rates of over 200KHz, which should allow for plenty of headroom.

This also assumes the signal from the HAL sensor is symmetric, which is should be isn't it?

The one downside is that it means you are constantly needing to read the ADC value.

As I see it, it's just a simple program that needs to be written. The logic for calculating the wait times can be done on a PC. Are you considering storing the timings in the EEPROM memory? That way you could simply upload a new set of timings, without having to rewrite the program memory. Or even go as far as having a serial interface that allows replacing timings on the fly while running.