Habit Training a Teenager on the Spectrum

I’ve mentioned my daughter in different threads. She will be 14 in May and was diagnosed with PDD-NOS when she was 12 1/2. I know we are late in ‘getting the ball rolling’ for her. I broke my ankle shortly after the diagnosis, so that pushed me back even more. I wish I would have understood a long time ago what was going on with her. It would have spared us several years of tears in homeschooling. Needless to say our homeschooling has been very inconsistent and I regret that. But, here we are and I really could use some words of wisdom.
I think I have pretty much decided on what we will be using this coming fall for school…..CM☺ My DD is working primarily at a grade 3-4 level. My question is habit training. I know this should have been done at an earlier age, but I feel we need some help in this area. Her diagnosis put her on target age wise for vertical processing (crystallized intelligence/strength), but at a 9-10 year old horizontal processing (fluid intelligence/weakness). So, this means she may act like a 13 year old outwardly in some ways, but her logic/reasoning/understanding (making connections) is well below her biological age. So, I need to be careful that I don’t do things with her that she would consider ‘ babyish’. But, I feel we need to work on habit training. What would be the best way to approach that with her?

We have a few friends/family members who do not understand her special needs because she appears outwardly to be a normal 13 yo. So, when she refuses to do something because she thinks it will make her uncomfortable or may hurt her, she cries and refuses to do it. She has sensory processing and overload issues as well. Or, she literally has made herself sick in the stomach getting anxious about going to a friend’s house without me. She is very self-conscious since she hit puberty. Some are looking at it as a disobedience issue, or she is too emotional, or she has an attitude problem, she is self-centered, etc. My husband and I are praying for wisdom to know how to handle these situations and to know how to help our DD. It has been difficult knowing what to do. I am getting a handle on the academic teaching, but the emotional, sensory, and attitude problems still need work. She also really needs help with time management. She is very loving and for the most part complies. But, she will resist if asked to do something that makes her uncomfortable. So, we have been accused of giving into her whims. We know we have failed in certain areas, but not all of these problems are just a matter of her sin nature. It’s difficult to discern what is and what isn’t sometimes, but with some there is not much grace. How can we help our special needs teenager in these areas?