I agree with the other about him being constipated. My daughter had similar issues(bellyaches, butt hurts, having pee accidents) and thats all related to constipation. Our dr prescribed mirlax.. Try to have your child drink more water, and less drinks with sugar. I kknow kids at that age really probably prefer drinks that taste good, but once we stopped giving our daughter so much gatorade, she seemed to do a little better...... But definatly see your own personal dr, I think.
About the rash, is her wearing pullups at night? If so, my children would ALWAYS get a rash on their bottom from were the pullup was, and that could be just from sitting in urine all night. Try Eucrin (sp) cream.