SignalsGuy, Here are some links that may be helpful.
http://www.crossfit.com/cf-journal/crossfit_validity_041.pdf
The above links to a report that compares participant results in the Crossfit program versus the AFM program. To summarize, the benefits for the Crossfit program were superior:
1. greater core and strength
2. reduced injuries in subjects (2 instead of 6)
3. equal the performance gains with less than half the running
It is extremely important to note that the "increased education level of the Crossfit instructors assisted in the Crossfit group". Therefore, there could be a bias there.
I myself have looked at the Crossfit program and I think it looks great, but it is too complicated and I don't have access to much of the equipment. Therefore, I am following the Army Fitness Manual with a couple adjustments. Namely, the running.
The AFT suggests running 5 days a week. 3 of those days are speed workouts. All of my education says that 3 high intensity workouts a week are very hard on the body and will greatly increase risk of injury. My own experience speaks to this: I get knee and shin splint pain when I do sprints or intervals but am very comfortable with LONG slow runs. Since I am already training for a half-marathon, and I'm not into injuring myself, I am following a different running schedule than that outlined in the AFM. I do 1 aerobic interval or speed workout, 1 medium intensity middle distance run, one long slow run and one fast short run. That's it. 4 runs a week.
If I go cross-country skiing, I will sometimes substitute it for one of those runs. However, the long slow run is never substituted. It's sacred. It builds a strong foundation for muscles and ligament strength and increases endurance. The short, fast runs are good for increasing aerobic capacity and speed.
Regarding the weight training component of the AFM, I've made a couple small changes. I do 2 leg workouts, not 1 a week as specified in the manual. Furthermore, I still add pushups at least twice a week. Finally, I mix up the weight training. I follow the AFM but do Circuit 1 of weight training for 1 week, then Circuit 2 for the second, then Circuit 3 for the third. Then back to Circuit 1. This keeps the muscles 'guessing' and works more of the stabilizing and secondary recruiting muscles. Dynamic movement is superior for conditioning - which the thought process behind Crossfit. I apply this same logic to the weight room; free weights are better than exercise machines for overall (core) conditioning. However, exercise machines are a good place to start if you aren't used to weight lifting (safer, more controlled movement until you develop a base).
Here is a link for you explaining the benefits of Crossfit:
http://www.crossfit.com/cf-download/Foundations.pdf
Good luck.
