Ok, I admit that maybe I misunderstood. I thought you meant create some sort of peripheral card for the Arduino, one that performs the MPGuino functions as an add in shield module to a Freeduino/Arduino module. More of a snap together assembly from available parts.
From your design, it seems that you are adapting the ATM168 and creating a single purpose unit for the MPGuino. That can be good for the long term, and I agree, with a programmed chip, it could work!
Maybe add tie points for the 4 inputs: VSS, Injector, ground, +12v. Either through some buss bar, or solder holes, and point labels.
Don't forget the MPGuino name, board version, etc.
Does the Eagle software maintain a parts list?