I think the overwhelming statement that is made on this site, is go where you are loved. If multiple coaches told me that they loved my kid, but they constantly pointed out his lack of size and strength, I would be really concerned. At that point, I would be more concerned about son's future. Therefore, D-3 and education would come first.
in most cases, I think education should come first, and in the case of your son, I definitely think it should come first. Too many things working against him. First, the fact that very few make it, his injuries, his lack of size and physicality, etc. Think education first, and hope for the other things to come along. If they do, great! If they don't, great too! He will be in a good position for his future.