Well, if you have Candida and you take a grape fruit seed extract before bed, you might feel worse for a while because of the die-off. Some other things to consider, are you hungry when you wake up? It could be that your blood Sugar is getting too low. Try eating a snack with some protein before bed, like some cottage cheese or an egg or some nuts.
Also, I was living in a house with a low level carbon dioxide leak in my bedroom for three years... Do you have gas heat? I would get a carbon dioxide alarm just in case.