DaddyO just so you know, Fenway is the guy here. Even though I know much less than he's forgotten I'll wade into say 2 things.
One, I think your son missed the boat. If he wants to play baseball at a top academic D1 I think his best option is to take a gap year and work in getting recruited for next year at Ivies, Patriot league schools, etc. With his academics, worst case scenario is that he has to go through the trouble of re-applying to the UC's and others again.
Two, sometimes you get lucky. There's a local guy who got recruited by Cal Poly in late spring after they lost players to the draft. But that's an isolated incident He was coming back from TJ and no doubt he had been on their radar before that.
Oh, and 3 - there will come a time when we all regret giving any weight at all to the US News rankings when helping our children decide where to attend college.