So I organize stuff for a living (I'm a project manager), but back when I was a student I was terribly disorganized, scattered, and spacey! Here are some tips that may help you and your DD get through this.
First of all, figuring this out is a process. Make sure she knows it's OK to try stuff, keep what works, and jettison what doesn't. If she changes something and it doesn't work, she can go back to her old system. She's probably terrified of changing anything in case the problem gets worse. If she's afraid of missing assignments during the experimental period, maybe you and her counselor can work with the teachers to be a backup for her (which I bet you are anyway).
Second, my DD also has a very large school and a locker in an obscure location. Not having time to drop by between each class may be accurate. But it could be that your DD just doesn't have the skills to put together a plan. For example: Go to morning classes with the red binder, visit locker before lunch, and then take the blue binder to afternoon classes. That said, my DD insisted for years that everything must be in one location. If your DD can remember to visit the locker just for her instrument, that will lighten the load considerably. I like the idea of alarms. If phones aren't allowed, maybe a watch or tiny non-connected digital organizer?
Third, it's better if she owns as much of this as she can. That means selecting supplies that she loves and trying to create processes that she can manage. You can be the backup reminder and provide support during the habit forming stage. Let her try to think of ideas that might work for her (and try not to judge them, who knows what will click).
Fourth, middle school is a time when teachers have embraced the idea of helping form organizational and executive functioning skills. This is great, but sometimes they have their own systems or requirements. Make sure your DD has help integrating these into her own larger system. Nothing like finally getting your kid to write down all assignments in one place and then have one teacher insist they fill out a special calendar or planner.
Fifth, be prepared to experiment with supplies. For example, a three hole punch (there are even little ones that clip right into the binder) can be great for keeping loose papers in check. Plus shopping for supplies can be lots of fun and engender a sense of ownership. DDs high school actually hands out planners to all incoming freshmen, but DD insisted on having a much prettier one that she picked out.
Finally, if your DD is resistant to change, make little adjustments. For example, if loose papers are a problem, maybe a single folder/pocket/pouch for the loose stuff seems less overwhelming than an entire new system. Then you make a habit of going through the pouch every afternoon and putting everything where it goes. The process of asking and answering a regular series of questions together: what is this? what do I need to do with it? where does it go? will help her start to do it more naturally and on the fly.
