What could cause headaches and clay-colored stools?

Clay-colored stool: Bile & your gut's bacterial flora account in large part for color & volume of stool. Absence of bile results in pale, clay-color stool. Lots of other things also affect stool appearance: ingested foods, medications (peptobismol, antacids), swallowed blood or bleeding from gut, infection/antibiotics, inflammation, maldigestion, & the amount of mucus mixed with stool, as well as transit time of food.