Watch the portal. It will tell you what's in and what's not. And keep in contact with your ALO.
Have YOUR SON (NOT YOU!) stay in touch with his GC. Make sure they have sent the forms (let's say by Oct 16th) as requested. Have him, in writing, let the GC know ALL his deadlines. Usually USAFA won't hold the school's delay against the applicant but it is your son's duty to stay on top of all of that. NOT YOURS. This will hold him in good stead later, and take some of the pressure off you.
Perhaps in the last week of October, I might give the ALO a heads-up/status update.
This may help you all keep on track: Make a big wall calendar (ours, with four homeschooled kids and four in college) and put it up in a visible place. Ours was beside the door to the kitchen that everyone went through every day. Keep it updated with ALL deadlines, events, etc, at school, church, jobs, sports, etc. We color coded ours but your mileage may vary.
Keep ALL the college infor there (his plan B schools, plan C, etc). Then, there is no question about what is due, when. I advise against keeping this on a computer or phone, though it can be there too. The wall calendar is there for everyone to see, and makes things more real.
Best of luck. Please let me know if I can help in any way.