I have always been prone to shin splints in the early stages of a running program until I can comfortably lengthen out the stride a bit, and with age my knees have become more susceptible to discomfort. My rule of thumb is to quit running and walk the balance of the time/distance when I start to become uncomfortable (from whatever cause - ragged breathing, side stitches, shin splints, etc) to the point where it affects my stride. Basically, once I'm unable to remain in the "comfort zone" I start to compensate with muscles and joints that I really don't want to be straining, so I avoid straining them. I also do a few weight exercises to strengthen the muscles so that the muscles take up the slack, not the joints.