What you are describing is the normal behaviour of a ball python. I think you are expecting too much out of a snake. Your snake will learn to tolerate being held by you but it won't want to be held by you.
"It is like she is very scared"
"She knows my scent and trusts me(I think)"
Those last two words are the most important in those statements. It's what YOU think. That format mean it's what our snake feels. Your snake will never trust you. It will tolerate you. You aren't gonna be buddy buddy with a snake. That's just not how they are. They are great animals but it seems like you are expecting a more interacting/affectionate animal then they are. Enjoy what you got and you will just learn to love them for what they are.