You sound like a strong candidate for admission. If I were you, I would not worry about paying application fee in the first place. Apply for assistantship or fellowship and this will take care of everything. US universities are spending so much money on international students. If you are really worried about application fee, try the universities in Florida. Application fee is really cheap compared to northern states. I remember paying 65$ application fees in University of Minnesota 4 years back, but universities in Florida charge around 30$ now.