(A) Why was it that the first two years... were chosen?
Irrelevant. The "why" doesn't change whether the results are valid or not.
(B) Did some of the boys... grow less than five inches?
Irrelevant. The argument is based on averages. Outliers (kids who grew less or more) are already accounted for in that average.
(C) How much do the average [students] in a coeducational school grow...?
CORRECT. This provides the necessary comparison.
If they grew 5 and 4 inches respectively in co-ed schools too, then single-sex schools have no special effect.
If they grew only 2 inches in co-ed schools, the argument is strongly supported.
(D) Did the girls... have as nutritious a diet as the boys?
Irrelevant. This compares boys to girls. The conclusion is about the environment (single-sex vs. general growth), not whether boys grow faster than girls (which is biologically expected anyway).
(E) What was the average height... upon entering?
Irrelevant. The study measures growth (the change in height), not the final height or starting height. Whether they started at 5 feet or 6 feet doesn't change the fact that they grew 5 inches.