I feel your pain. I've dealt with this issue for more than 30 years of running. It doesn't happen on all runs. The nausea and pain for me is almost always associated with an increase in distance and/or stressful intervals. Many times (when I was younger and trained harder) I would get back from a run and just lay on the couch and hold my gut in pain. Just awful.
I went through all kinds of tests. I was scoped with cameras from both ends. I drank barium to allow xrays to track fluid movement through my digestive track. Tried eliminating foods for allergies. Nothing ever turned up.
The bad news is my doctors eventually gave up and just called it some type of exercise-induced Irritable Bowel Syndrome (IBS). You can find a lot on this online.
Over the years I've associated various foods to increasing the likelihood of a problem. High fiber foods like carrots or even peanuts can trigger an issue. But the biggest trigger for me is abdominal stress...and when I run hard I can almost guarantee I'm going to have this problem.
The good news is "running hard" shifts as I got more fit. The intervals that blew up my gut a month ago don't bother me because my fitness improved so that workout is less stressful.
Best of luck. It's a tough problem.
Me three. Any kind of hard and/or long run workout will have my stomach in knots; Iâ€™m sprinting for a toilet once per week and suffer from several bouts of diarrhea after particularly hard runs and always after races. I havenâ€™t been able to get a medical answer or define specific triggers, but itâ€™s been particularly bad the past 6 months as my mileage has increased. A crappy problem, and a pain in the ass ;)