For an object traveling through air the rise time of the photo transistor is effectively irrelevant, you just need to measure the exact moment when the signal hit's it's peak, if both sensors are the same then you measure the distance between the two peaks and you're all set. Not sure how you would interface this to a sound card, but if the projectile is small and you simple feed the transitor output into an or gate you'll see ticks on the sounds wave form corresponding to the interuption occuring and then ending. OR'ing both inputs together and you should see the two peaks you need to measure the distance. At 44.1khz you count the number of samples between peaks, multiply by the reciprocal of 44.1 khz and you have a very accurate time stamp. If you have really slow photo transistors increasing the distance between the two points to perhaps 5 feet will help separate the two peaks. Should be pretty easy to test.