stlish -- I am NOT a doctor . . .
So you used the date "31 January" as the deadline for application documents . . . I'm assuming that is 31 Jan 2019? . . . and you are applying so to be selected winter/spring/summer 2019, and enter in June/July 2019 with USAFA class of 2023?
If my assumptions above are correct, you should go ahead and get all of your application paperwork done prior to 31 January. You have to do a certain amount of the application before USAFA will schedule you for your DoDMERB exam anyway. I think I would work with the USAFA Admissions POC you are assigned to, and let them know your condition. They can advise you, and might be able to make things work so your DoDMERB exam doesn't happen until after 22 Dec 2018 . . . and perhaps happen soon after the 22 Dec date . . .
Make sure you rehab well, and get in shape for, and practice the CFA . . . You will (or should) need to have that done and submitted prior to the DoDMERB appt
Others on the forum may be able to provide better, more informed advice, but it seems if you did DoDMERB exam prior to 22 Dec 2018, you will be DQ'd . . . and it is not clear to me how they would clear you with a medical waiver prior to 22 Dec 2018 . . . it seems they want to see how stable your knee is a year after surgery . . .
If you wait to do DoDMERB until after 22 Dec 2018 (and berfore 31 Jan?), and the knee is stable . . . seems like you would be good to go with DoDMERB awarding a "Q" with no remedial, or perhaps there will be a need to do a remedial to double check the knee and provide some paperwork . . .
You are correct, the timing is a bit tricky . . . IMHO, definitely talk with your assigned USAFA Admissions POC and get their advice . . .