Been there done that. For the notes, one suggestion that worked for us was to have her try to write her own notes, but to also make arrangements go get a copy of another student's notes who is a good note taker. Might also want to look at a product called the Live Scribe: http://www.livescribe.com/en-us/
A planner helped with organization of school work. Fortunately, for us all the students were required to use it so there was a specific time during each class where all students took out their planners and wrote down homework assignments. We had a buddy system where one of her friends would do a double check to see that she wrote down the assignments correctly and update any changes required to reflect the assignment due.
With the room, it is still an ongoing process that we haven't totally come to terms with, but decluttering and keeping it down to essentials has helped somewhat.
Reading is easier to remediate than self-esteem. It is good that she is talented in music and sports. It is important for kids to realize that we all have strengths and talents -- whether or not we have a disability or not. Not all o us are good cook, or golfers, or mathematicians. We all struggle in some way or another. Each person develops at their own pace -- sometimes it just a matter of time before we each find our own wings.