Matt, you can start asking people to write letters of recommendations--you'll need 3 letters for AFA (probably similar for other academies), some for your MOC's and maybe ROTC. Check all requirements as some will want certain people (HS counselor, principal, one of my son's MOC's wanted a peer). You don't need 15 people, just pick 4 or 5 that you feel will be able to write a good letter that can speak to your character, leadership abilities, etc. Each letter can then be used (addressed appropriately of course) for more than one academy/MOC/etc.
You can also start requesting medical records from doctors/hospitals/etc. if you know you have a medical condition or had something in the past (surgery, dislocated joint, allergies, eye problems, etc.) that could raise a red flag with DODMERB (not just the sniffles). If you Google DODMERB remedial codes, you should be able to locate a list of remedials. Just don't assume the worst, though, if you see something on the list that you've had in the past. Many things just require documentation of problem, treatment or therapy, and current status. Other things may require more testing. DODMERB remedials can take time to clear up, so if you have the medical history paperwork already on hand when you take your DODMERB physical this summer, you'll be able to send it in right away when requested.
Also, you can start putting together a resume of all your activities, honors, sports, volunteering, etc. during your HS years. The AFA, MOC's, and AFROTC all requested one when my son applied. Keep updating it, though, over the summer/fall as you continue to do new things, get awards/recognition/etc. for something.