I have had problems along the lines of what you described with my sleep cycle most of my adult life. You may want to have a sleep study done to determine if you may have a mild case of sleep apnea going on (this was my diagnosis). I have trouble using CPAP and I got rid of the machine. I just deal with it and I do take the NyQuil equivalent when I am really sleep starved.
Here is an interesting link to Harvard Medical School’s summary of the external effects on the sleep cycle: