1. Does your bicycle fit you properly. Has it been set up correctly for you?
2. How strong is your core? The stronger your core is the more comfortable you'll be on a bicycle over longer distances.
3. Have you tried a wider saddle? Just because you're short doesn't necessarily mean you've got narrow hips/sitbones.
BTW - gel and cushioning aren't usually good choices for saddles. Maybe when you're just starting out, but not once you start to do longer rides.