I would suggest mixing up your running. It’s a one mile run, so try to do a lot of track type workouts, like running 400m sprints at a 1:1 interval (rest for as long as it took you to run the 400m). Distance is good, but don’t worry about the 2 mile until after the CFA.
For pushups, try pyramids. Try to get to 10. Do 1 pushup, then 2, then 3, up to 10, then back down. Rest in the leaning rest position for a couple of seconds in between each set. Also, find out how many you can do in two minutes, and do sets of half that number. Say you did 60, do sets of 30. Eventually, try to do sets of half as many as you want to do for the test, so if you want to do 70, work up to the point where you can do 3+ sets of 35. Make sure your form is good, even if that means doing less pushups. Don’t cheat yourself, because even if it doesn’t hurt you on the CFA, you don’t want to get into that bad habit because you must have perfect form for the APFT.
For pullups, just do as many as you can, but get someone to spot you and help lift you once you can’t do any more by yourself. That’s where the real improvement happens.
Both the shuttle run and basketball throw are as much about technique as fitness. The key to the shuttle run is quick turns. For the basketball throw, it’s all about finding the right trajectory so that you get maximum distance. You don’t want to “laser” it, but launching it like a mortar isn’t going to get it very far either. I played baseball in high school but found this event very difficult. Understand that your hand can’t touch the ground in front of you until the ball has hit the ground, but try to lean back and throw yourself forward as you rotate your shoulder.
I see that you will apply for the class of 2014, so you have a ton of time to increase your fitness. Stay consistent with your workouts and you will be fine. Good luck!