You asked the question and multiple people are sharing that the GPA and SAT are definitely red flags to coaches. They won't know or care or give him credit that he's in an aviation program for 60+ hr a week - they're measured on team grades and keeping players eligible.
Multiple schools during my son's recruitment had 3.0 GPA across core and 1000 SAT - MINIMUM. Definitely retake gotta get those up.
Check out Kranse Institute. They have some great study tips and tricks and it's written by a guy who aced the SAT/ACT and does everything in short burst videos. https://www.kranse.com/
Have you tried posting videos of him batting on @flatgroundbats or pitching with stats and measureables @flatgroundapp? They are great to help spread the message if he is uncomfortable speaking for himself.
That might be another item that causes concern to a coach if he isn't willing to market and stand up for himself. Cocky is never good, but he has to be able to market and show for himself to these programs.
They want to hear from him not the parents. It's tough. We help get them to a point but then have to let them drive and we can "Back seat" them as much as possible.
The JUCO route is not a bad option. Lots of schools LOVE their JUCO transfers. (Arkansas, Texas A&M, etc). Get some good grades and exposure underneath him and transfer to a program is an option. Get him in a program, put on some weight, add to his pitching package and velo and you should be good.
Don't burn your bridges. Tight nit community. Someone is always watching. Get the word and videos out on Twitter and you'll get something.