Usually a stomach ache or stomach cramps are a result of eating too soon and too much before a run. I would not eat within 40 minutes of running. I also wouldn't eat a huge meal before running either. I usually run in the morning and have a healthy breakfast and then start running about 40 minutes after wards. Also don't drink too much water or energy drinks while running. Water is OK but some of the energy drinks can make your stomach ache while running.