Two quick things in addition to prayers for your son's health... the West Point Moms page has not been nuked, lol, it is very active and an incredible resource... and I believe that there were some in the class of 2023 that had trouble commissioning because of medications that they were put on...
Yes, we had to send in a check. It was rumored that if a cadet candidate could not pay it, that they could contact USMA and it would then be taken out of their pay over time. I don't know if this ended up being true.
My DD is class of 23 and yes, we had to pay a $2000 fee. There was a spot for it to be checked off right in her portal. It was explained that it offset the cost of the issued items at Beast.
I can't speak for this cycle directly but two years ago my DD received her nom from Senator Schumer in her USMA portal on 2/2. The letter came in the mail after.
If the candidate is under 18 it will change to received for the immunization form but the circle will remain red until they are given the last vaccine on R Day. Confirmed that with cadet health services.