First a baseball thing. 4.2 to first and an 8.3 60 don't mesh. One is major league speed. One is snail slow. I completely question the person doing the timing.
I'm betting the story isn't exactly as your son told you. More than one coach is upset with him. There isn't a conspiracy to get him. Your son has to suck it up and talk with the coaching staff about what they perceive he did wrong.
My son was a varsity starter soph year of high school. When the bus stopped for a game the coach made a public announcement regarding my son that completely caught him off guard and humiliated him in front of the entire program. My son's response? I may never get to tell the coach. But I'll show him he's wrong. That's how these situations should be dealt with.
Its normal to want to know the situation about the varsity as your son approaches the opportunity. But you can't just buy into every negative point you're told. You have to completely understand the circumstances before being able to access the claims. Whatever you do don't poison your son's mind with other people's opinions.
As the father of an 8th grader I don't recommend starting a coup against the coaching staff. Leave that to the upperclassmen varsity. You don't want to kill your son's chances before he has the opportunity to make varsity.
Sometimes coaches have difficult personalities. If they're breaking the rules and running off players the Board, Superintendent and AD notice. I don't believe for a second a coach threatened to hit your son with a clipboard unless he was smiling and joking about it. Otherwise it's assault. He could lose his job.