Does she have the intellectual disability component? If she does, that's something a number of moms here will identify with, even if their dc doesn't have NF1. Also we've had people dealing with children with concussions, head injuries, or challenges after chemo, sigh. You can google site search the boards by putting in the terms and site:welltrainedmind.com into your google bar.
It sounds like you're doing the right things, getting evals, figuring out what is causing what. Those headaches sound very hard! Personally, since they are physical in origin, I don't think I'd tell her tough it out. I think I'd use multi-sensory where you can, so she's building more pathways. That way if one hurts, she has more paths. And I think given how strong she is with auditory you're going to want to use tech. Audiobooks are awesome here.
Use your Mother Gut and keep it positive. If one path isn't working, say that's ok and try another one. If one area isn't working, say that's ok and try another. Get some balance where her day is 50% what works, not 90% what doesn't work, kwim? Channel to yourself the confidence you would have if you had done this before and knew you knew what you were doing. There's no reason to think someone else's opinion is better than yours or more valid than yours about what is good for her and healthful and what is creating good balance. So go with your gut and create a radical, beautiful, healthy, peaceful, positive balance for her, no matter what that looks like.
Make some goals. Like if she's happy, healthy, growing in kindness, caring about people, able to pursue things she enjoys, able to solve her problems, increasing in independence to the level of her ability, these are good things! For my ds, his reading improved partly because he needed it to do things he wanted to do, that independence piece. So maybe let it come naturally together for her. The materials you're using sound good if they are clicking. If they stop clicking, people can suggest some disability-specific options. There's always another level of detail and support.