I'd first modify the circuit to connect +5V to pin 4 of J3. This will make programming the '328 chip easier. Then build up the PCB.
> Never tried Arduino
The Arduino part takes a few steps. Start with an ATmega328 chip that's preprogrammed with the bootloader, plus a FTDI Basic module that's needed to program it. Install the Arduino IDE on your PC, load the Arduino_Light_Flicker_Measure.ino program, plug in the FTDI module and select the corresponding port in the IDE, and finally compile/upload the code.
The front end electronics are the tricky part in this project; if you are good with electronics it should be fine for a first Arduino project.
What kind of Arduino? If it is an Uno that uses an ATMega328 chip in a socket (and can be removed) you can reprogram the chip directly from another Arduino. This was one of the first links I found for doing this but a search for "programming atmega328 using arduino" should show you more. Alternatively if it is that kind of board you can also order the IC's pre-loaded with the bootloader. You could then put that into your arduino and use that setup to reprogram the original '328.
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Hope that Helps,
ripred
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From the seller '12V application'.