It sounds like you are doing a wonderful job with her. Taking it slow and easy is the best way to do it...even with horses that aren't abused or mistreated. She will learn to trust you...although it sounds like you are already gaining her trust.
I use a clicker and treats with my gelding. What a wonderful training tool if used correctly. I highly recommend it! You can make great strides with horses that are motivated by food! It is a great way to get their attention and get them focused.
Keep up your great work. It sounds like you are on the right track. I would just continue what you are doing...breaking every new bit of training into small pieces so she doesn't get overloaded or stressed. Set her up for success.