A couple of things to aim your attention to.
1. Your WCS includes everything. They will look at the rigor of the school and the rigor of your course load. If your school only offers 5 APs, and you took all of 5 of them, you won't get marked down because the school across district lines offers 10 APs. You took what was offered.
2. If you go across district lines, before you do talk to the GC. What if you can't take those additional 5 APs because you need pre-reqs. This is now going to hurt you, because the AFA board will see you didn't take the most rigorous courses offered. It wasn't that you weren't trying to, but because of transferring so late, you couldn't. They can't see that, they can only see what you took, and what was offered.
3. Leadership and EC's. Starting over means fresh. You are the unkown to the school. You are not going to become Key Club President as a jr there, because nobody knows you. You were never a member off THEIR Key Club, however, at your old school, they do know you and you could get a leadership position as a jr. Same with athletics.
4. As military towns go, because the rate is @30% turnover every yr. kids come and go. Cliques exist in hs, but there's a difference if you are not from a military town. These kids have gone to school with each other since they entered 1st grade. They have built their friendships, and it is hard to break into their groups because again you are unknown. School is more than academics, it is social. Our DD was forced to attend a new hs when she became a jr. (we moved because of the military). When I say she hated us all that 1st yr., that is not a lie. Every fight resulted in with these words, "why did you make me move, I want to go back". She is INCREDIBLY social, we call her the social butterfly, but because for the 1st time she went to school that didn't have a military base filling it up with students, she found it difficult to make friends. It took her to early spring before she found her footing.
Best of luck in your decision.