When you are finished with the R&D stage and ready to install this into the blaster, Instead of using the Arduino pro mini. I would follow this http://arduino.cc/en...inoToBreadboard and simply burn the bootloader and sketch to a ATmega328 chip. This will save you some cash as well as a little space. The ATmega328 chips run around 3 US dollars instead of the Arduino Mini Pro which is close to 20 US dollars.
Using your arduino to program chips is not very difficult at all. I use mine to program ATTiny85 chips all the time.