Batsmith - I get it. You're frustrated with the lack of response you thought your son would get by now. Join the club.. .
Many of us have been there, and it isn't a good feeling. When I was in your shoes (5 years ago), we made some major modifications to our strategy and all of the sudden things changed overnight. For us, it was leading with academics & baseball rather than just baseball that caught some coaches attention.. Possibly, your son is in a similar position or has something that can separate him.
Getting recruited as a college shortstop is a tough road. While the hs SS experience is phenomenal, I'm not so sure a SS who runs a 7.0 / 60 is going to be a positive metric for him in college. College coaches may project him as a CIF or COF. My point is that it may take a college coach with some foresight to project him there (CIF or COF)and take a chance on him making the transition. Many college programs will recruit SSs that can hit. Initially, they'll move them to outfield in college only to bring them back to the infield when they are more seasoned. Obviously, I've never seen him play. But just be aware that your son probably playing the most difficult position to get recruited in college.
Do you live in CA? Where is your son looking to get recruited...CA? If so, you may want to expand that search somewhat as CA & West Coast is probably the toughest place to get recruited....there is that whole supply vs demand thing out there that is ridiculous. You've already found an interested East coast academic school. Did you follow up with that East coast D3 school and all the schools in its conference?...you've found a good place to fish....why not fish there some more! If nothing comes of it, try a similar strategy with schools in a similar type conference. Keep trying and trying until he finds his niche.
Others can help on this site with ideas, but the best solution is going to come from you and your son. Step back, because somewhere in front of you is a better way to approach this recruiting puzzle. Good luck!