"only 100 microseconds" is equivalent to up to 1600 AVR instructions.
That's really quite a long time.
It's quite a short time if you have to guaranty that an A2D conversion occurs during this window to ensure detection.
I think the O/P is going to need some sort of threshold circuit to generate clean digital pulses. A simple comparator would be fine, with the inverting input set at 4V, then the non-invertinng input gets the 5V .. 3.5V signal and the comparator give you a nice clean rising edge suitable for generating an interrupt.