The Gerber files will be given to place the parts on the board.
Which parts? Which board?
My question is how Arduino will read and interpret these files and translate the order to the stepper motors to pick up the part and place it on the board.
Arduino does not read or interpret Gerber files. The stepper motors will not outomatically pick up any parts either. And the Arduino without further hardware will have trouble driving your stepper motor as well.
This is not trivial and this is what you will have to figure out...
Will the Gerber File need any type of conversion to be read by Arduino?
Again, Arduino does not know what to do with a Gerber file.
I recommend you start programming with an arduino, work through some tutorials etc.
Sorry that I am not very helpful, but your questions are so broad that it is really difficult giving any usefull information without doing your project for you.