Thank you all for the prayers, I'm really hoping for a simple fix.
Sometimes I think no history is better. I know basically how my mare was treated, this is a very public case and it is still currently active (the guy hasn't been sentenced yet). I know there was over 120 horses on roughly 80 acres and the guy was bailing ditches along the highway for hay. She was always hobbled for breeding, so she had a serious issue with people touching her back feet. I am not sure how many babies she had, I might be able to look that up if they were all registered.
I don't think she was abused physically as it only took a few months for her to let me do anything I want to her. But I'm not so sure of some of the other horses there. She has become just the sweetest mare ever and all my hard work paid off, now if I can just get some weight on her.