Things to do:
Ensure that you are competitive. Do well this year. Reach for leadership positions. Be awesome. If you are not competitive, you will not be considered for a medical waiver. On the other hand, if you are LOA material (and the condition is waiverable) you will immediately be considered for a medical waiver.
Finish the application as soon as possible. All of it. It opened right after SLS in July last year. Once you complete most of your application, call your liaison officer, if he or she has not already called you. Start prepping for the CFA at SLS, if you're going. Knock it out at SLS, or by September.
The thing to realize is that not everyone who is medically disqualified will even be considered for a waiver. Make sure you are competitive enough for waiver consideration. That starts with a strong and complete application.
I had a similar experience applying for USNA. I got a status letter informing me of an approved medical waiver yesterday. Do everything you can, and things will hopefully work out. Even if they don't, at least you did everything you could.