In my experience, a lot of those side effects can come from prednisone. I had some real joint/muscle pain on pred, and my hair falls out during/after the taper, though Imuran (related to 6mp) has thinned out my hair somewhat (I've been on Imuran for 4.5 years). Given the abdominal pain you're having, talking to your doctor certainly couldn't hurt!
Diagnosed with Crohn's in April 2003 (first symptoms in 2001).
Current Medications: Imuran 125mg/day, Humira, Pred 2.5mg/day, Cortifoam, Phenergan as needed for nausea (have previously taken Asacol, Entocort, Flagyl, and Cipro)
Dietary Supplements: Flax seed oil, Folic Acid, B12, Culturelle