OP, I think you are doing a great job of trying to sort out a lot of conflicting and strong advice. It seems you made a mistake, quite possibly, resulting in the likely pregnancy of the filly. Well, here's my thoughts;
you wanted to breed that stud, right? well, you probably did. So, allow the foal to be born, geld the stud and work on the filly's behavior issues, and, ultimately, either keep all three as pets, or look to rehome one of them (now well trained) after the baby is here. And if baby is a colt, geld him so you can have a peaceful "herd".
With the filly, look at making her respectful at you at feeding time. That is the first place to start. Work at requiring her respect before you give her a drop of food. Never allow her to come in take a bite until you have moved her away, stood over the food 'claimed' it, then, after making her wait, move off and allow her at it.
Then yoiu do the same thing, but you go up and pet her before allowing her to have at the hay. I don't know if you said she was aggressive at food time, but getting her a bit hungry and using access to food as a reward for submission will be a good starting point. http://www.youtube.com/watch?feature...&v=xfFxYgY_5g0