I was supposed to MSAF 5 days within the missed midterm, which I failed to do so. Instead, I used the online MSAF form on the 6th day, which only let me MSAF the 13th at the earliest. Im stuck, and my prof still won't reply.

In that case, you should go talk to someone in your associate dean's office ASAP. Since you have a valid reason, I think it will work out in your favour. Just to be on the safe side, you should get your physiotherapist to say that you are still in pain like you mentioned before. Hope it works out for you!