A few things. First, what are you currently doing training- and diet-wise? How long have you been doing that and what kind of progress have or haven't you seen? What do your lifts/PFT results look like? Without knowing where you are it will be hard for people to help you.
Second you seem to think that your "body structure" and "metabolism" are somehow unusual and require some sort of special training program. This is highly unlikely. Any reputable beginner's strength and conditioning program should work for you if you follow it consistently and back it with proper nutrition (assuming you have no significant injuries/conditions etc). No program is going to cause you to "accidentally" get "huge" and "ripped", trust me on this. Whatever your goals, you will benefit from building a decent strength base as it will make you better at everything else. You accomplish this by picking up heavy shit and putting it down, preferably in some sort of logical progression. WS4SB, 5/3/1, Starting Strength, these are all well respected programs. There are others as well. Pick any one and follow consistently it for at 3 months while eating properly and you will get stronger. You will not blow up and get "huge".
Another consideration, as you are military, I assume that your fitness testing is centred around running, push-ups and pull-ups and sit ups. As such I suggest that you might want to train for these. Push-ups/pull-ups can be done daily, broken up into small sets whenever you can fit them in. Recon Ron is a pull-up progression that many people swear by. Some people also swear by adding weighted pull-ups 2x/wk to boost max reps 1-200 push-ups divided through the day is fairly easy to fit in and I suggest an equal number of stretch band pull-aparts to keep your shoulders healthy. An intelligent running program should include a mix of speed and distance work, but it really depends where you are now. As I understand it military PFT's are based on 1.5-3 mile distances, so 10k/marathon training is probably not really the most important focus. I would be reluctant to train sit-ups regularly due to the risk to your back. here is a link to a good core training article:
Regarding your goals, You have fat loss as priority one. At 6'4" 200, depending on your bone structure and body composition you may or may not be all that fat. I would suggest that you train for your performance goals, eat a decent diet (meat, vegetables, fats and starches in reasonable proportions etc) and let your body fat sort itself out. Here's a basic nutrition article. I don't know how much control you have over your food choices day to day but it provides some guidelines:
As for striking speed and conditioning, intelligent bag-/pad-work and sparring and to a lesser extent general joint health and mobility are going factors IMO. All other training is a distant second as far as this goes.
So, a sample program COULD look something like this:
-5/3/1 Mon/Thur split as per this article: http://www.T-Nation.com/free_online_article/most_recent/531_reloaded
-Running program 3-4 days/wk (I like running in the morning)
-Recon Ron Pull-up Plan as per your ability daily - takes about 10 min
-1-200 push-ups 100 band pull-aparts daily (sets of 10-20 every few hours)
-Include some rucking/farmer's walks/sled pushes and/or drags either on 3 non-lifting days or as a "finisher" following your 5/3/1 sessions as your recovery allows
-Fight classes bag-work etc as scheduled
-daily mobility/foam roller work
All of this will need to be tailored to your current fitness level and recovery abilities. With this type of volume you need not fear that you'll get too huge. Of course, I'm just some dumb-ass on the internet, so take all of this with a grain of salt.