The biggest problem I'm trying to overcome with my horse right now, is that she is an off the track standardbred, and a rescue from severe neglect and abuse. She's healthy now, but we're working really hard on trust. She was VERY afraid of her head being touched when I got her, but now shes has no problems with me putting the bridle on or her taking the bit, and every once in a while, she'll actually give me her head for a good scratch. So it's coming, but still being worked on.
What you are doing is great! I know it takes a lot of patience to get a horse to trust again. I had a mare that was abused by males. From the time I got her, no male could go near her. After I sold her, the new owner told me that she stayed that way. She had to have female vets, farriers etc.
I had one like that. He wasn't a rescue; we just think he had a few brain issues. He was cute as a button, unfortunately, he didn't like being a rideable horse.