OK, this is what i think, for what it's worth. There is a similar post in Secondary School section.
She may feel a bit overwhelmed with the amount of things/new routines that she now faces. She can't be expected to learn in a few weeks what we as adults have become used to over years. So she needs help. I read that a habit takes 30 times of doing it to acquire it as a habit (if that makes sense). So for now, you might have to help her more that you think you should. But the proof of the pudding is in the eating -she needs help.
So, what can you do? In my view children get very stressed and that is awful. I know of too many young children who are feeling stressed just now, and with an already anxious child I don't want to make things worse, so without apology I do things that some other parents do not need to do. For some children this would be 'helicoptering' but all children need different things, there is a no 'one size fits all'.
For your DS, maybe all the responsibility is a bit overwhelming, and you need to show her by example how to manage it. When she has (or feels she has) thing under her control maybe she'll be better able to focus on her work.
So -help her work out a homework plan, and a time for when she does her homework. Then ensure she sticks to it -if it's a struggle, then try to make a nice routine -a drink and snack of her choice/your agreement? And some reward for when it's done -this depends on your timetable, whether you can fit in a nice time on the sofa watching a short TV programme, or whatever she likes. Or whether you add it all up into a weekend treat.
Make sure her bag is packed for school next day every evening. She will do this but you need to ensure it's done. Maybe give a checklist, so she can see what's she's done (i.e., packed bag? Phone charged and ready for next day? Zip card/travel card in usual place? All homework in school bag? PE kit in bag?
Make sure her clothes are put out every night for her to put on in the morning. Same for PE kit. (I don't see this as teaching learned dependence, I see it as a joint effort which needs more of my input at the moment but which will be slowly transferred over in time.)
So this takes away the added stress of getting ready for the day.
Next, work. Make sure she has enough time to do each piece of homework. tell her to do each bit to her best standard. No music or TV (obviously).
Also talk to her about her school day -is she struggling? How does she feel about being Head girl -would she care if she lost that? What does she care about? What subjects does she love/hate/flourish in/struggle in?
Is she getting enough sleep? That could be a major factor? Does she eat breakfast (sorry, I know this is obvious -but low blood sugars affect concentration). Does she have a cod liver oil supplement? Is she low in iron? Does she have enough exercise?
How much of this is 'her' (physical) and possibly hormonal? How much is environmental, i.e., her routine. Is she Year 6? Is she going through entrance exam prep?
Finally, you say you want her to take pride in her organisation. She will have a better chance at that once she feels she's good at it. She needs to see some success, so start with small tasks, like making sure her school bag is done properly every day. She might relax a bit when she feels it's under her control.
Anyway, other posters will have more suggestions. I appreciate much of what I have suggested you may already be doing, or won't be right for your DS. Good luck.