Have a look at these links:
http://www.arduino.cc/playground/Code/Interrupts
http://www.arduino.cc/en/Reference/AttachInterrupt
https://web.archive.org/web/20210413164913/https://www.uchobby.com/index.php/2007/11/24/arduino-interrupts/
The catch, though, is that if you have more than one coil firing, while you will know that the interrupt occurred, you won't know (at least, in the interrupt handler itself) which photo-transistor triggered it; in the interrupt handler you would have to check the pins assigned to generate the interrupt and poll (read) each of them (and hope that the poll happens fast enough!) to see which one generated the interrupt, then use that info to fire the correct coil.
If your projectile is moving too fast, from either the injector, or subsequent acceleration by the coils - then you might get a trigger on the interrupt, but by the time you poll the pin, the projectile might have moved past the sensor that generated the interrupt. At that point, your choices would be to either use "direct connections" as you noted, or use a faster processor.