You need to help us understand what "it doesn't work" means. Do the wrong pins go HIGH/LOW?
pinMode(ShakePin, OUTPUT); //Shaker Relay Pin
pinMode(ShakePin, LOW); //
pinMode(FeedPin, OUTPUT); // Feeder Relay Pin
pinMode(FeedPin, LOW); //
pinMode(StopPin, INPUT); // Cutout Switch
pinMode(StopPin, HIGH); //
Let's see. Is HIGH equal to INPUT or OUTPUT? I'm guessing that the second statement in each pair is supposed to be digitalWrite(), not pinMode().