KmomNH,
I have been where you are and fully understand your concern. I also like the approach you are taking.
My son was the same way in high school. He had a 'dream school' in mind and that school was very interested in him. His grades were marginal at best, but he thought that good enough. In the end his dream school passed on him for other players who would not be an academic risk. Schools are less likely to risk losing a scholarship because a player can't meet the academic requirements once they are in the program.
Good news...my son ended up at a very good JUCO program. His dream school kept up with his progress. Not his baseball progress...they kept up with his academic progress. In fact, during the recruiting periods they didn't even come to see him play. When they were allowed to contact him they asked about his grades. I don't think they even talked to him about baseball.
He has worked extremely hard in the classroom and is on track to graduate from the JUCO this coming May. His dream school invited him for an official visit and offered him a very nice scholarship. He will enroll there in the fall.
While we have been very happy with the JUCO program which has terrific coaches, if my son had done his job in the classroom in high school he would have had those two years to learn the program of the school he originally wanted to play for. His time there will be shorter but he is looking forward to it. He knows now that in order to stay there he will have to make the grades. He doesn't want to be responsible for the school losing scholarships because he didn't do his job.
Best of luck to your son. It sounds like he is heading in the right direction. Stay patient.