If you use a proper comparator you won't need any resistors because you can compare against the 3v3 supply.
From your description it sounds like the 1->0 transistion can only happen at one place in your waveform, so use that as a trigger. The AVR input pins have some hysteresis if I remember correctly so that should help (unless too much noise).
if the op-amp circuit works i'll be hoping to push that 1v up to as close to vcc as it will go so yes, i'll trigger there.
Where is that signal coming from?