This is time for you to evaluate your own relationship with her. If you are unwilling to stick by her long-term, this would be the time to exit the scene. I think her efforts to "pull back" are her way to allow you to do this.
I've told her that I'm in this for the long run, and I want her in my life for as long as we possibly can. She has trouble believing it, but says that it will come in time.
I'm young, but I'm steadfast in my beliefs. I've had close family friends with MS and Huntington's, and I know generally what our future would be like. Yet I want nothing more than to be there for her, whatever it takes.
I think you are correct when you said:
She kind of wants to be left alone, but I'm not sure. That just seems like a sure way that she'll end up depressed.
I would suggest that she needs more attention now than ever.
She's no longer allowed to speak to me for the time being. Great.
Anyways, if this all does eventually work itself out, can anyone give me more details on what to expect in the future? Maybe even things I can do to be proactive instead of reactive?