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.