It sounds like your D has made great progress but is still not fully recovered. I don’t think a rec from a 9th grade teacher is a great idea, unless she has maintained meaningful interaction with that teacher.
Your daughter has already put three years of high school behind her. She can’t change her transcript.
She hasn’t pursued the most rigorous courseload, which is absolutely fine. She should ensure she applies to colleges that are not expecting the highest rigor. I am sure her recommendations will be good for the types of colleges she can apply to based on her existing transcript.
A great rec is helpful, but it can’t create rigor. So in a way, it isn’t super important that she get a second amazing rec. I suggest she ask an 11th grade teacher who will “do no harm.” It’s very possible that a lot of the colleges she will apply to will only ask for one rec, in which case she can submit the one from the English teacher. Best of luck to her.