That kind of stuff is always hard at first. One of the reasons I can never get into jogging is because it kills my shins.
I've never had swollen ankles before, though.
I used to get that too, but I stopped stretching before running ( walking 5 min, start jogging slowly is how I warm up) and no more shin pain, calf pain or lower back pain from running.
That was when I was 18, now I'm 36 (and 265lbs, about 18% fat) and still have yet to have any pain from running.
Though I only run about once per week. Other cardio other days.