I know you said "enough" on the advice but I had this thought earlier that I think may be helpful to you and, possibly, your son.
A few times now, you have correlated how well your son pitched with expected acceptance of him as part of the program. As a HS coach, I want players who can perform well. But, I demand players who can be good teammates and behave up to the standards we set for the program. I don't care how good the kid plays if he can't be a good citizen, representative of what the team stands for.
I am more than understanding of young teens acting like young teens but there are times that some make decisions that are worthy of just sending them home and letting them "get right" before they return. And, when it gets to that point, it is almost never the first time an issue has come up with that particular young man. Again, I don't know if that is the case here with your son but it is starting to sound like it is a possibility to be aware of going into your meeting.
Lastly, I am always one of the first to suggest letting the kid handle things himself and it sounds like you are as well. But, in this instance, where there may be a behavioral issue (on the part of the player OR the coach/es) and where there is this much confusion and disconnect, I actually think you should meet with the coach. I would want the player present, though, so that everyone leaves hearing the same thing and hopefully being on the same page going forward, if there is a going forward. In fact, I would also want all three coaches involved to be included if possible as well.
I can give you several real life first hand examples that support this.