Couple of points:
1. There is plenty of time once he gets healthy. My son had mono(Jan-Feb-early March) and was visiting schools in April of his Sr year and had colleges coming out to this HS games during the season.
2. Revise the plan and figure out SPECIFICALLY which schools fit him.
3. Realistically JC's don't really recruit until later in the HS season, but start to work on a back up plan.
4. Put in applications to schools that fit his profile.
5. Get real on his ability. My son plays for "only a D3" and I can tell you that no freshmen is going to crack the OF unless he is an absolute D1 stud. It is that competitive at highly ranked D3's, They have three spots for graduating Sr's and they will be filled by returning players and some freshmen will get some spot playing time here and there to build for the future.
6. The possibilities for playing in college are endless if you look in the right places. Go to d3baseball.com and REALLY look into all of the programs, there has to be one there that he can play at and more importantly fits him academically and culturally.
7. Let the D1's that were following him know he was injured. My son was connected to all of the D1's that were following him at the Arizona Fall Classic and he let them all know he had mono when he got it.
I know it is stressful but revise the plan and keep working it, there is still plenty of time.