Six weeks is way too long to have recurring diarrhea and not to have a diagnosis. You need to see a doctor now with a view to having an endoscopic examination and a definitive diagnosis.
"Pancreatitis
In addition to causing stomach irritation (gastritis), drinking can inflame the pancreas. Chronic pancreatitis interferes with the digestive process, causing severe abdominal pain and persistent diarrhea --and "it's not fixable," Saitz says. Some cases of chronic pancreatitis are triggered by gallstones, but up to 60% stem from alcohol consumption." (webmd.com)
I think you need to see your doctor about this. Workout hard at the gym should help your cardiovascular health, but won't touch this issue imo.