I will tell you one thing that I'll wager you won't like, but if you will take it to heart, I assure you it will help.
You are doing too much for your son. Many of the tasks you describe yourself doing are his job. The fact that you are doing any of the work for him identifies some key problems.
First, the fact that your son is tired and doesn't want to work on the paperwork so you do it for him: If your son cannot handle this level of workload, he is not cut out to be a D1 player. What your comments say to me is that he likes playing baseball but he does not have a full appreciation for what is involved in the event he actually reached his goal. Players typically come home exhausted day after day, and then they open their books and they do what school requires of them. Day after day for every day for four years. We are not talking about recreational baseball here. We're talking about baseball as a job with school always imposing still more workload.
Conversely, if he thinks he is a D1 player, then the time has come for him to start proving that he has what it takes to manage his life and all the responsibilities that come with his choices all on his lonesome.
Second, to the extent that anyone sees you doing all this for your son, you are not helping him, you are hurting him. Partly because college coaches see all they need to see of helicopter parents while recruiting, they would just as soon not have them around for the four years the son is playing. But also partly because when it becomes clear to them that a kid does not fully appreciate what it is he's asking to be taken into, what will be expected of him, and a determination to meet his obligations all on his lonesome, that is a kid who has a higher than average likelihood of washing out in college. And given the choice between two otherwise comparable players, your son will lose out.
I noticed that whenever you mentioned that you were doing things for your son, you prefaced your comments with an excuse for doing so. What that tells me is, you've already heard this message before and you have decided that it really doesn't apply to you because things are really tough in your particular situation. What I'll tell you is, you are wrong about that.
If you really want to help your son, show him this note and tell him that from now on, it's tough love, and he's on his own.