Took me time to read whole thread (and it seems I was part of discussion?)
2 new links for ChuongNhuka
http://www.crossfit.com/cf-journal/AOFP-Austere-Program_equipment.pdf
www.military-pentathlon.org/Download/Obstacle_guide.pdf
I would agree that you need to do as homework your GPP (general physical preparedness) and do together team skills.
Don't forget to create benchmarks. Test your benchmarks every 3 weeks and use 4th week as recovery week (still train just instead of 100% intensity scale to 70%, if you weren't at 100% in your workout week you don't need recovery week). Your team also needs to setup benchmarks, that everybody need to have, if they are not up to requirements than they need to work up to it.
Your GPP training is 20minutes to 1hour, what you do in your specific activity/sport helps, but it is not part of your GPP.
Activities to increase upper body strength:
Pushups - aside from regular, lets do variations on weight distribution, one leg in air, raised legs, one arm, one arm-one leg, handstand;
position of hands, elbows move parallel to body, hands bellow chest, bellow face, wider than shoulders, above head, knuckle pushup;
plyometrics, pushup jump, clap pushup, tripple clap pushup, whole body jump, power overs;
hindu pushups, dive bomber pushup, pike press
Equipment, blocks (power over, raised legs or 3 blocks for legs and arms, this is deeper pushup), resistance bands (good for speed training), T cross good for wrist strength, weighted vest (or backpack)
Pullups, chinups; alternating grip, narrow grip, wider grip, on thick bar (like soccer goalie post), one arm, hanging on towels (or ropes), claping pullups/chinups
This is just a sample, you will find more on Net.
Endurance interval training, 100pushups/500squats, 100burpees, hill sprints, rope jumping, tabatha intervals.
To improve running, think again intervals. Lets say you have 2 mile run but competition speed is 11-12 minutes. So try first 1/8 mile run but at competition speed (1:23 - 1:30)x 8 sets, next time try 1/6 x 6sets, 1/4mile x4, 1mile (5:30-6:00) x2.
Would concentrate more on endurance than on strength. So alternate type of training focus like strength-endurance-power-endurance, same thing with type of running like distance-distance-sprints.
You can also chain exercises in sets like pushup-crunch-squat-chinup-superman-lunge (rest), whole idea is just to keep speed. And for warmup 2-3 minute max.
Exercise plan is good for 3-4 weeks before you need to change it. Change, rest time, number of repetition, type of exercise, resistance.