You have a shot for an appointment at both SA's. USNA: if you are a Principal nom-that’s a golden ticket as long as you meet USNAs requirements (USNA still has to want you). #2 on a Ranked Slate for USAFA, means you have a Nom and if #1 gets Appointed and charged to that MOC, then you are still in the running for USAFA from the National Wait List (lower chance of appointment but still a chance).
Principle Noms essentially mean that the SA is going to Appoint you if you meet the SA requirements (3Q). Sounds like this MOC uses some sort of "pre-interview" call / process. That’s unusual. Since it's a pre-interview...you may not get those ranked nominations after the actual interview. We don’t know what we don’t know about this particular MOC Nom process.
BGOs are not permitted to influence how an MOC determines nominees, however, I find the pre-call process troublesome-unless they are giving you a hint of what they want you to change. Seems to me the pre-call process places a lot of pressure on candidates prior to the actual interview. Perhaps phone the MOC contact and ask: If I change my ranking to USNA first, does that help guarantee a Principal appointment.
Understanding that your fist choice is USAFA, having a Principal Nom to USNA is a great opportunity that very few get. Maybe take the sure thing...and follow the MOC staff's advice-you are not appointed until you are appointed.