First of all, your son looks like a great applicant. He has obviously worked very hard in school, and I’m sure that colleges will recognize that!
As far as his GPA, colleges will take the middle school grades out of his GPA and recalculate it.
I have some suggestions:
1-Replace the LAC group with a safety group. The LACs that you listed have very competitive applicant groups and you cannot count on him getting in to them easily. Safety schools should have acceptance rates around 60-70%. Pick one or two of your state schools for these, or a private school with a high acceptance rate.
2- I rearranged your college list a little:
First group (most competitive):
-Duke, Johns Hopkins, Rice, Washington, Vanderbilt, Notre Dame, Pomona, Bowdoin.
Second group (more likely to get in):
-Emory, Boston College, Case Western Reserve, Carleton, Davidson, Washington and Lee. (A lot of these schools have acceptance rates of close to 20%. You may want to add more schools in the 30% and 40% range.)
Third group (safeties):
-None yet (1 or 2 schools with acceptance rates of 60-70-80%.)
Best of luck! He is a very competitive applicant.