I really need help... dominant-submissive 3 year old Pit Bull....

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My dog came to me recently - she is around three now (according to the vet), and I have only had her for 3 months. It is fairly obvious that she has been abused in her life. Even though she is 80 pounds, she was so skittish when I first got her that you couldn't even really get close at all or touch her without her running away. She also had third stage heart worms, mange, and such a build-up in her ears that she was practically deaf. We got the ok two weeks ago that she is heart worm free - to the tune of $2000 USD, I nearly fainted when we got the news (not because of the money) - I didn't even know exactly how stressed out about it I had been. I started crying because, like it or not, I became and have become very attached to this wonderful dog right away. We have gotten past most of the obvious problems - she is finally starting to eat kibble and drink water when someone else is in the room. She has stopped running from me or anyone else altogether, but now wags her tails and approaches although cautiously. My PROBLEM: Because she was sick for nearly all of our time together I was terrified to discipline her very much - she could barely walk and she couldn't sit down without crying out in pain. She is totally fine now though to the point of knocking me over and rampaging through the house like there is no tomorrow. I have read all the stuff about the "dominant pack leader" and am trying to follow the advice. I don't let her walk through doors before me anymore and she must sit every time before getting any food or a treat. BUT, she is so dominant AND submissive. If I raise my voice even a little bit she crouches down and puts her ears flat and shies away like I am going to beat her. It kills me to see it, BUT she has also started shoving through doors ahead of me and she is BIG into staring competitions and they really unnerve me, I don't show it though, I just stare her down, never blink first. I am so torn between feeling bad for her that she had a crap life and now I am starting to think that maybe she is just playing me. After 3 solid months of my company (I work from home and we rarely leave the house except for walks and going to the park), she sleeps on my feet in bed (yes, it hurts all 80 pounds of it), and we are never apart. I worry that I am messing her up by not giving her independence and she is really doing this passive-aggressive thing. I'll go to pet her and she rolls onto her back with her feet in the air and is totally submissive - two seconds later she is knocking me out of my computer chair and pushing me with her nose. I am not sure what to think except that I am the proud owner of a psychologically disturbed dog... I MUST emphasize here that at NO TIME ever have I ever felt threatened or in danger from my dog. BUT, I do not feel secure at all that I can control her - she walks Beautifully on a leash - UNLESS she doesn't want to. She only comes when she feels like it, and can really give the cold-shoulder if she doesn't get her way - not for an hour or two, but for up to two days and abstain from food to prove her point. I am lost as to what to do, should I be more firm and get her to behave or just give her more time to acclimate to a non-violent atmosphere where she is too-much treated like a Princess. She is very responsive usually, and somebody must have really trained her as she knows over 15 different commands and will perform if food is involved. I just don't know what approach to take. Also, if I could afford to go to a good dog training school for obedience classes, I wouldn't be asking for help here. I welcome any and all advice or, at this point, even commiseration, Thanks for reading this long-winded vent,