I think you really have to experiment on yourself to see what might be causing the stomach pain and what might alleviate it. For me, it depended more on what I ate the night or morning before a long run than what I ate during it... complex carbs, or just too much food, seemed to be particular culprits. I had to carbo-load, just not too enthusiastically! But others have contributed that what they ate during, or even after, the run, contributed to stomach pain more than what they ate prior.
I'd try to analyze the whole course of my nutrition, before, during and after the run, and try to vary one factor at a time. I do think that stomach pain after a long run is fairly common, although generally speaking with careful attention and experimentation, you can figure out a way around it.
Jane in CT