Ralph has a list of foods he should eat every day: 1) bread and butter 2) milk and cheese 3) meat and eggs 4) fruits and vegetables 5) citrus fruit (fruit that contains Vitamin C)
When you "go over" something in your mind, it means you are mentally "reading through" the list; reciting the list so that you will continue to remember everything on the list; thinking about the things on the list; looking at the list again; and in this case, reviewing and checking off the things which you have eaten and making a mental note of the things which you have not eaten.
"At night he'd go over the five food groups and see how he'd done that day." At night he would review the list of five food groups to see how well he had followed his healthy eating plan that day.
"For it takes five fingers to point the way to healthful eating habits. And Ralph GOES OVER them in his mind. " You can replace GOES OVER with any of these to arrive at the same meaning: REVIEWS THINKS ABOUT CONSIDERS
"At night he'D GO OVERr the five food groups and see how he'd done that day." You can replace 'D GO OVER with any of these to arrive at the same meaning: 'D REVIEW 'D THINK ABOUT 'D CONSIDER