redhen, it could be something you're wearing. Somtimes birds are afraid of glasses or baseball caps. Were you wearing either? Certain patterns on clothing can drive them crazy too. She might warm up to you over time.
They do get mites. I rescued an Yellow Crowned Amazon about 15 years ago. Same type of situation. The cage cups were so filthy I left them behind. I remember having to scrub down the cage and perches several times - it took hours. Casper? Became Maria. She is well over 40 years old and when I...