What's the PWM rate? If it is slow enough (relative to the CPU execution speed) then have the PWM also trigger and interrupt and read it during the interrupt.
If the interrupt isn't at a convenient time, start TWO timers, one for the PWM and the other one for the interrupt. If the PWM is constant frequency they should stay in sync.
If the PWM is too fast, then just have the ADC sample all the time, and pick the right ones in software (the maximum, minimum, ones at the end of the on-slope or whatever).
Or add peak-hold hardware and just read the peak voltage if the control loop can handle the filter.
Tom