Where do you describe why football has a lower APR than other sports? Are other sports not dealing with missions and athletes who could be struggling with academics? I don't see anything in your post that specifically discusses football.
Aside from baseball, football was the only program at BYU that fell under 960. 932 cannot be explained by your analysis. The coaches must be accepting players with lower academic standards than they are in the other sports for this to make sense. I guess you could argue that football is just too demanding and that's why football players struggle. But why do football players not struggle at Stanford? It's because they only accept players that meet a certain academic standard.