What to do?

I have been w/ someone for almost 2 years now, and most of that time we have been long distance. He is a good person, but there are lots of problems b/c of his inability to deal w/ unpleasant things in life and his lifestyle (He has legal issues..nothing scary, just the run of the mill bs that our judicial systems throws at those who are...uh unconventional, but these issues make it even harder for us to see each other now).
And then there's me and my problems. I was raped twice and haven't really dealt w/ it. The first time that I tried to talk to my bf about it, he changed the subject. He has talked to me about it since then, but never knows what to say and is visibly uncomfortable. I have also been fighting a horrible case of candida for the last three years. My health condition has got me really depressed. I am trying to get my stuff together. I started a grad program and completely stopped drinking. I got really serious about fighting the candida and have been dealing w/ a lot of weird stuff b/c of that...detox, die-off, depression, emotions. Initially, my bf told that my illness was all in my head...of course, most people told me this until I found this site. My bf now tries to be supportive and says that he believes that I am really ill. He deals w/ my mood swings pretty well most of the time.
But, I feel like I'm at a point where everything needs to change. I've changed locations, lifestyle, priorities. I want to get well...and I'm afraid that our relationship is toxic. He has tried to get better...stop drinking, stop getting in trouble, get his shit together, put our relationship first...but all of this just started happening. I feel like it's too little too late. I love him, but I also really hate him sometimes.