None of the 3 academies you listed have any soft disqualifications. The only academies that do are USNA (they have one) and USAFA (they have many which you will no longer be able to view).
Once the other SA's add your son's name to the DoDMERB database, you will be getting new status letters that will include the new SA.
I'm not sure I understand exactly what you are asking. You have seen a soft disqualification on the DoDMERB web site? Or did you go through the list of disqualifications and find ones that may apply to your son?
If I wasn't able to answer your questions above, let me know and I'll attempt to sort it out!