I usually wake up in the mornings feeling horribly nauseous (I would say 5 days out of 7) . . . I am not sure what it is from, but I have been that way all my life. I absolutely cannot even think about eating when I wake up and the even the smell of food makes me want to throw up. All I can do to deal with it is take it easy for a while, wait for the feeling to pass. Usually after I have been awake for 2 or 3 hours, the feeling is gone. I don't know if it is IBS, though - I have never been tested for it . . .
I also have frequent headaches, similar to what you described with the sharp pain and the sensitivity to light and the severity of the pain on an "ebb & flow" type cycle, and that dreaded nauseous feeling as well. And they are STUBBORN headaches that just do not want to go away. Even if I can get them to go away, they leave me feeling just trampled.
My doctor recommended a combination of ibuprofen and antihistamines and the combination seems to work for me. Allergy headaches can make you sensitive to light and will cause pain behind the eyes, in the forehead and wrap their way around the back of your head as well. Allergies can also trigger migraines.
Have you ever been tested for allergies? This may be something you want to ask your doctor about since if your headaches do turn out to be an allergy related thing, it is pretty easily remedied.