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Don't discount the importance of physical fitness in being able to defend yourself. If you are strong and fast, you can move faster and strike harder when the need to fight arises. Sometimes self-defense is as simple as striking a vulnerable target with sufficient force to incapacitate the bad guy - hit lightly and you might just piss them off. As an example of this, why are Navy SEALs such dangerous opponents? It's not because the h2h fighting methods they are taught include some magic death touch. They are supremely well conditioned both physically and mentally, with a never quit attitude that is selected for through a difficult training pipeline.
Physical conditioning is an important part of training. I recommend training for strength, speed, and endurance. Regular weightlifting and body-weight exercises are good, as well as running, swimming, and cycling. For running I recommend both long, slow distance runs as well as interval runs (e.g. spring 100 yards, rest, then repeat 5 to 10 times). For a beginning athlete, I recommend the following schedule to get started with running. This is almost the same schedule that Naval Special Warfare recommends aspiring SEALs follow to prepare for the rigors of BUDS (Basic Underwater Demolition/SEAL training).
Week 1
Run 1 mile each day, rest on the weekend
Week 2
Run 2 miles each day, rest on the weekend
Week 3
REST. Your body needs time to acclimate to the stresses that running puts on your legs and your joints. Cycle, swim, lift weights, do body-weight exercises, but DO NOT run during week 3.
Week 4 and beyond
Continue running 2 miles each day. Work on improving your speed. Also, every two or three weeks you can increase the distance of each run by 1 mile. If and when you get up to 9 mile distance runs, that is probably as much as you really need. My own distance runs are usually only 2 or 3 miles depending on how much time I have available to train.
Below is the training schedule that I follow myself
Monday, Wednesday, Friday - strength training (squats, pushups, situps, pullups, bar dips, calf raises - all just using bodyweight), running
Tuesday, Thursday, Saturday - commando combatives
Sunday - yoga, practice commando combatives with a partner, sprints (100 yards x5)