Need help with timing circuit for ballistic sensor
I think you can use the built-in input capture in the AVR microcontroller (possibly with an Arduino library function rather than bare-metal programming). If you did have to do the latter, Atmel Studio is a free download and has everything you need software-wise.

Timer 1 is 16 bits and, I believe with minimum prescaler it can be run at 16MHz (assuming that's the CPU clock), which gives you 62.5ns resolution and 4ms maximum time. The counter free runs and the count is grabbed upon seeing an edge when properly configured. 

The only problem I foresee is that the pulses may be two close together for the input capture to be reconfigured to grab the second edge on the other input pin. In bare metal programming you could use an interrupt and probably some microseconds would be enough. At 1500 FPS you would have 111usec for 2" which sounds like a lot of time for an ISR. You could get about 1776 counts which is likely much more than necessary or even useful. 

For that, or other reasons, you might consider increasing that 2 inches- it seems rather short to get high accuracy anyway. Commercial bullet speed meters use more like 200mm/8" IIRC.