Sounds like you want to do an exercise program like I am starting. Its StrongLifts.com 5x5Advanced lift schedule
It includes 3 lifting days for a 9 week program, including volume phase (4wks) and then intensity phase (4wks) with a deload week between
The schedule is....
medium squat, heavy bench, heavy power clean, weighted dips
Light squat, OH Press, Heavy DL, weighted pull ups
Heavy Squat, medium bench, medium power clean, turkish get ups.
Im only on the second workout, but it looks complete. You can get the whole program (you can punch in your numbers and it gives you exact weights and sets to do for each) at StrongLifts
Add max effort sprints on Tuesday, long run on Sunday, and pick 2 days to run up to 3 miles in the morning and again that night @ 80%+, lets say mon and Friday.
that gives you two complete rest days, one before your heavy squats (and to recover from the DL) and one before your long run.
From what I know about military runs, they are usually pack hikes of long, 20+ mile treks with heavy weight.
Definitions of "long runs" can vary. 3 miles is still considered short for me. My LSD runs would be in the 20 mile range.