From my experience attending a 'high stress' academy in SoCal and helping prep recruits for another, you will need to be able to do high reps (i.e. 400-600 push-ups/day) of body weight exercises (push-ups, squat thrusts, mountain climbers, sit-ups and pull-ups) and run distance (3-6 miles at a <9min/mile) 3x/week. The ?CrossFit? types of workouts are during the PT sessions. The body weight stuff happens at every at march-on, breaks, lunch and any time someone screws up.
Honestly, the minimum PT tests/qualifications were not a big deal for an active recruit compared to surviving a day on the 'beach'. My class saw the weight room about 3 times in 26 weeks and there were no "tests" on any lifts. So for the majority of your prep workouts, reduce the weight room unless you need to rehab/prehab something. Do your BW REPS!!! Get back to the iron after the academy. Focus your prep to succeed at the academy.
Focus your basic prep workouts on body weight exercises (push-ups, sit-ups, squat thrusts/burpees, mountain climbers, pull-ups and running) with the idea of multiple sets of 25 reps (except for pull-ups). Oh...and they are back-to-back sets meaning 25 push-ups, 25 squat thrusts, 25 mountain climbers, 25 sit-ups...repeat with ~10 second breaks between sets.
Two simple ways to get in reps: 1) during the working day, every hour take a break and bang out a set of push-ups. You can dive under your desk or an unused conference room. Pre-academy, I worked in a professional business environment and did this in a shirt and tie. If anyone asked, I told them it was my version of a cigarette break.
2) at night when you are watching TV, every commercial break do a set of push-ups and one of the other exercises. It?s pretty easy to get in a few hundred reps each evening. Or if you are watching baseball, do the same at the top of every inning.
A good prep program is the SEAL Prep on www.navyseal.s5.com/workouts.html. Feel free to skip the swimming portion.
As for a good starting program beginner?s running plan, check out the "couch to 5K" program on the Cool Running website. If you are already beyond this level, pick one of the other programs. Save yourself some pain, head for a runners shoe store (not Dick's or Big 5) and have them find the right shoe for you. It will cost a bit more but it's worth it.
Another suggestion head for a boxing or muay thai gym. The conditioning aspect is outstanding and you can develop some cross over skills along the way (i.e. hitting things). Don't be too concerned if the most accessible place to you isn't a MMA hotbed as long as it isn't KardioKickboxing or whatever your gym is calling the aerobics class. You should be hitting the bag or pads. An UFC gym would do you fine.
You could certainly sign-up for CrossFit a few days a week if you want to get use to that type of program.
Remember: we don?t typically loose people because they can?t pass the PT TEST. If recruits leave because of PT, it?s from the constant pounding throughout the day.