I cannot stress enough that at this stage of the process, most of your questions can be answered
OFFICIALLY at USNA.edu.
Open every drop-down menu and read, read, read. Click on every yellow
LEARN MORE box.
The Admins and Mods here will do their level best at making sure that the answers you receive to questions here are accurate, but be advised that some answers or advice will be from a decidedly narrow vantage point.
What I mean by that is that most members will be more than happy to share how they got through whatever you just asked a question about, but their case may be specific only to them.
What was approved or waivered last year can have very little bearing on what will happen this year (and by "year", I mean the 11-month cycle which started yesterday and may not end until April 15th next year with Offers of Appointments, or Thin White Envelopes stating "better luck next time" or words to that effect).
The application process takes time. There are no awards for getting your application in ahead of everyone else, and your application will mean very little without a nomination. All Members of Congress (MOC) have different dates at which they open up their nomination application process (sometime in the Summer), and those nominations aren't typically handed out until November or December.
So take a deep breath. There is plenty of time to get all the items of the application done. Keep at it, and continue to chip away at the stuff you can do yourself, while you wait for your end-of-year academic transcript to be sent to USNA. (among other things out of your direct control).
Oh yes - if you haven't started already - you should run. One thing you will do a lot of in the military, is run.
@Capt MJ will help me out here.