Man, can I relate to those symptoms! The late night waking could be due to over-active liver functions which happen somewhere between 2am and 4am. Toxins. I have both fungal and parasites which I believe are somehow connected.
The parasites of most concern are protozoa--specifically B. Hominis.
They result in unevenly digested food, indicated by crumbly or clay-like stool. And in my case, there is itchy rectum after each bowel movement, and this sometimes continues throughout the day.
I have exhausted my means for controlling symptoms without success. So perhaps someone else can be more helpful at suggesting a plan of action. Shroom