Contact your ALO and ask him/her. Yes, athletic coaches can do the CFA, but it's always good to coordinate these things so there's no confusion.
As for when to submit the results, each person is different and needs to consider their entire package. Personally, unless you were on the border line of passing/failing the CFA, I wouldn't wait. A couple more sit-ups or pull-ups is not going to give you any advantage. Your CFA isn't as significant as many other areas. The CFA is basically a Go/No-Go section.
In other words, if you can throw the basketball 75ft now; throwing it 80ft in 2 months isn't going to make any difference. Shaving 20 seconds off the run; adding 3 sit-ups; 2 pull-ups; etc.. is not going to give you any real edge or advantage.
The application process is a "TOTAL- PERSON" review. They are looking at
academics
athletics
public service
leadership
physical fitness
attitude
communication skills
extra curricular activities
They also use the opinions of your teachers and your ALO to validate and verify consistency of your application. Your application AS A WHOLE either makes you qualified or not. If you are qualified, the process continues. You'll go from
PROSPECT to
APPLICANT to
CANDIDATE to
APPOINTEE (If lucky)
Generally, you are competing against others in your district and/or state. Your rep and senators aren't really going to care if you did 2 more sit-ups than the other person you are competing with. They are going to be looking mainly at your grades, SAT/ACT, school Athletics, volunteer time, leadership, etc... (Helps if you get your name in the paper, school lists, other notoriety.
So, why did I go through this long explanation? Simply because you need to look at EVERYTHING you do when it comes to your application. If your application is pretty much as strong as it's going to get:
I.e you are applying for the class of 2014 and your junior year grades are in; you've already been on varsity sports; you've taken SAT/ACT scores; and all the other categories; then I would be submitting your application as soon as possible. That includes getting your physical completed. Yes, the physical and CFA are areas that you really can't "REDO". But if the CFA is in the average or above of the scores the academy posts, then take it and submit them. You won't get that many extra points for a couple more sit-ups; but you will get extra points for an application that is 100% complete early. The official application process for the class of 2014 starts in June. If you are attending Summer Seminar, wait till you come back. Immediately put in for your physical. Coordinate with your ALO for your CFA. But it is quite feasible and possibly to have your application 100% complete; including CFA and physical; before the end of July. You should be able to be only waiting on a nomination. Assuming you are qualified by the academy. You can continue to take the SAT/ACT. Each score can only help you. It can NEVER hurt you. Continue taking the hard classes you were taking. And when the board starts looking at the 100% complete applications around 1 September; and yours is in there; you increase your chances of an LOA. But the board won't look at the application until it's 100% complete. The physical can take time and the nominations usually take time. But everything else has to be 100% or they won't look at it. For a prepared applicant; who's spoken with his teachers before school got out for the summer and prepared them for the email they will get; and the prepared applicant who has spoken with their ALO; there is no reason in the world your application can't be 100% complete before the end of July. Best of luck..... Mike.....
