While dehydration, a drop in electrolytes, especially sodium, and low blood sugar have all been attributed to muscle cramping, the reality is, there is little research done on this subject. In fact, no one is for certain the real cause(s) of muscle cramping. Because exercise is a stress on the body, that may be the biggest cause of cramping especially when the muscle crosses two joints, such as the calves (cross the ankle and knee). However, new research shows that some of us are just more prone to cramping than others and when we increase our training volume and/or intensity we begin to experience issues.
In a June 2011 study published in from the British Journal of Sports Medicine the most likely cause of cramping in conditioned athletes is muscle damage from increased intensity of your workout, while the most likely cause of muscle cramps in unconditioned individuals are due to lack of salt or water.
So what do you do? Ease into your training. Allow a good warm-up and practice interval training which will prepare your muscles for race day speed. While stretching may help after your workout, trying to stretch during your workout may actually trigger your stretch reflex therefore making it even more difficult for your muscles to relax.
As far at the issue with your shoulder, this could be like a stitch that occurs under your ribcage however, if you have not been cleared by your doctor to run, I recommend that you contact him/her just to make sure this is nothing to be concerned about.