This is not typical of dymenorrhea (painful cramps during
menses). Assuming your "stomach pains" while running are actually
pelvic area discomfort, there are a variety of things that could cause this,
including ovarian cysts, infections, and endometriosis (endometrial tissue
that is located in areas it does not belong.)
The best thing to do is to have a complete pelvic exam, with
cultures and possibly a pelvic ultrasound, particularly during the few days
before your period is due to see if there are anatomical reasons for the
discomfort. If all looks fine, then a trial of a non-steroidal
anti-inflammatory medication, like ibuprofen or naproxen, taken regularly
for the week before you expect your menses, might help with the exercise
related discomfort.