The muscles that hold your organs and whatnot in place need to be strengthened too. After running for awhile they will be strong enough not to cause stitches in your side anymore. If you do get a side cramp, you can try running bending into the cramp and clench the cramping muscles to help relieve it. Or bend away and clench. Depends on the cramp. But that can be done when running, if only a bit akwardly.
Doing your ab work before running is probably tiring out your internal muscles and making you prone to cramp. I would do the ab work after the run.
There may be other cramping involved due to nutritional issues (heavy food before a run isn't a good idea), but I would up the ab work, and not do it before running, and see if that helps.