I'm pretty sure most who have low cortisol are familiar with your sleep issues. I am definitely one of them.
Either cortisol or blood glucose (can't remember which) in the body is lowest at 4 am, thats why you wake up and can't get back to sleep. I used to suffer from this a lot when I exercised too hard or ate poorly during the day.
The trick is to get up when you know you're not going to get back to sleep, do your work stuff if possible until about 7 am and then go back to sleep until 9 am. Personally I've found that I am able to sleep again at 6.30. When I (have to) wake up at 8 am and go to work I feel just fine during the day. On weekend I just go back to sleep at 6.30-7.00 and sleep as long as I feel like.
Dr Wilson in his book "Adrenal fatigue" also suggest that you wake up, do something until you can get back to sleep and then sleep until 9 am and you'll be fine.