Is it only the positive pulse width you're interested in or are you trying to grab the positive AND negative? How wide/narrow are these 88 pulses? 100ms/88=1360us per bit?

Idea: Connect the pulses to a pin capable of generating an interrupt. When the first pulse comes along the interrupt is fired. Grab the first pulse "manually" using a count loop or a hardware timer, compensate for the interrupt latency. After the first pulse is grabbed, still in the interrupt service routine, grab the rest of the pulses using the same method you're currently using. Alternatively grab the rest of the pulses using the same approach as the first one.

This way you can do whatever in your main loop, as soon the first pulse of a frame comes along an interrupt will be generated and you will be able to grab it.

/Henrik.