High cortisol will cause waking in the middle of the night. That's exactly what I had to deal with. I was taking LOTS of melatonin, at one point 30mg. I also took phosphidtyl serine. Seriphos by Interplexus is the best form of PS that I've found. It was recommended on Janie's dessicated thyroid group on yahoo [http://health.groups.yahoo.com/group/NaturalThyroidHormones/].
If I woke up, I took another seriphos. I also took hawthorne to help with the pounding of the heart which can make it very difficult to fall asleep. Tryptophan is good too. I still take that if I wake up in the middle of the night. I also take lobelia too. Four capsules of lobelia will help me get back to sleep along with tryptophan.
You'll have to experiment with all of the above to find what will work for you.
I don't need the seriphos anymore, but I still use melatonin, lobelia and tryptophan to help me sleep when my back is bothering me.