velocity101:
I was originally planning on using the continuous illumination method and hoping to capture an IR reflection off the bullet as it passes up to a foot above the photo diode. Do you think this would work? Also, do you think that the 20us or so the bullet reflects above the photo diode would be sufficient to trigger a digital pin on an Arduino?
The continuous illumination method is simpler so it's worth trying first. The best way to trigger the Arduino is probably to use a rising or falling interrupt, that way it can response to very short pulses.