Hi there!
Excessive amount of physical exercise is associated with skeletal muscle spasm, more common in irregularly used muscle groups; that is responsible for stretching type of pain. This is commonly associated with some amount of inflammation which tends to get better in a few days. Severe exercise is also accompanied with some amount of dehydration which is responsible for abdominal cramps. However, it is abnormal to have an intermenstrual vaginal bleed. A few possible causes may include hormonal/ endocrine imbalances, ulcers, growths, cysts, erosions, infections/ inflammations, DUB, bleeding disorders etc. I am not sure how far have you been evaluated. A complete evaluation would include a physical examination, routine blood and urine tests, blood hormonal levels, an endocrine panel including a thyroid profile, imaging studies such as the ultrasound scan etc. I would suggest consulting a gynaecologist for the same. Meanwhile I would suggest keeping your body adequately hydrated while exercising. It is also important to do a warm up exercise before starting a work out. You may begin by running at a slow pace and then gradually increase your speed. On the days you are not working, try some other mild-moderate activity like aerobics, short walk etc. Try not pushing yourself to overwork. For pain management you may try some tylenol, NSAIDS or anti-spasmodics like dicyclomine. If these do not seem to help, you may consult your physician for hormonal/ stronger medications.
Hope this helps
Take care!
Did they check you for either Endometriosis or Pelvic inflammatory disease?