I will add one other point of emphasis to consider. I am not sure how highly regarded his pitching coach/instructor is or if that guy has any connections with college coaches, particularly D1s. If he does not, no matter how much good you think he is doing with your son, you need to get him into a training facility/clinic that has those connections. Ask coaches, particularly area college coaches, who they would train with.
I am going to assume that in Baton Rouge, there are some highly regarded training clinics. In SoCal, there are a lot of them, and I know one that is notorious for getting late risers signed by D1s (mostly mid-majors and lower but D1s no less). This facility does a lot of the intense training to boost velocity and conditioning and sets up kids well for strong senior seasons. The owner has a good pipeline of coaches, and he has some success getting late signs--I mean like May-June signs in D1s that lose recruits and players to the draft, transfer, etc. None of these kids would be playing college baseball had they not had that connection.
At this late stage, especially hearing about his high school situation, it is all going to be about having connections if he wants to aim higher than D3 or Juco. I agree that Juco sounds like the best option if your son is truly determined it has to be D1. But as others have said here, there are many reasons not to just focus on that. He needs to understand he is really late to be getting into the recruiting process for all levels other than D3 and Juco at this point.
Good luck and please go back to this thread and update it along the journey. You aren't the first parent to come into a situation like this, and this forum is an incredibly valuable place to learn about all of the different challenges in getting a chance to play college baseball. Your end result will help others learn in the future.