What can cause me waking up early cause of weird feeling or pain in stomach and sometimes a bowel movement? the pain is just above my belly button.

Bowel Blood Flow: I had a similar case before, which with vague symptoms, was hard to discover , But could be IBS, Transposition of the Superior and Inferior Mesenteric artery / veins ; Duodenal Ulcer ; etc. Need a complete GI workup

See a Doctor : Abdominal pain that wakes you from sleep can be many things from constipation to more serious conditions. You need to see a doctor in person to accurately assess the problem.