For waking up stuff, it might be worthwhile to get a sleep study, or at least have someone observe you while you're sleeping. I did a sleep study and found out I was twitching my feet all night long, which was waking me up several times an hour. I started taking a large amount of magnesium and that solved the problem.
I also have a problem where I hold my breath for several seconds, then wake up with my heart racing and pounding. Taurine helps the heart pounding, and B12/methylfolate are helping with the breath holding.
I have testing confirming that I'm deficient in all of the above, not to mention low neurotransmitters (serotonin and melatonin are the two that work with sleep).
In general, recurring dreams are the ones that are trying to tell you something. For a long time, I had disturbing dreams where I was back in school, trying to find my books, my classes, getting lost, thinking I had to take more studies even though I had already graduated, etc. I attribute this to all the research I do about the disease.
Other disturbing dreams take place in the house and neighborhood I grew up in.
Since I've started methylation, my sleep is deeper. It's been awhile since I've had those kind of dreams.