I can tell you are at the end of your rope here! Usually when a cat won't use its litter box exclusively, it's either a medical condition or stress. First of all, you need to have at least two (preferably three) litter boxes. One for each cat and one extra. Perhaps your girl doesn't want to use the box the boy does. Perhaps she doesn't particularly like the type of litter being used.
Second of all, don't punish your kitty. Cats don't understand that they've done something wrong. It just breeds fear into them. It's great that your kitties get along together, but there is something in the environment that is not sitting well with the little girl. If her stools are not normal and have not been normal, then there is something wrong with her. Bad bacteria or parasites can cause this. If your vet can't find anything, you may want to get a second opinion. She's not doing this to spite you. There's something wrong in her world and you have to find out what it is, fix it, and then she should be fine.
Female cats spray for territory. If your male isn't a problem for her, then are there neighborhood cats around that she can see or smell or are spraying around the outside of your home? Cats sense of smell is about 14 times better than ours, so they can smell things you and I can't, including an obnoxious litter box.
Good luck.
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