No diagnosis (been tested for both IBS and celiac, the whole shebang), but similar symptoms. I always get up early, it doesn't matter. This issue wreaks havoc with me when on a tour, as I just finished. I have to have one cup of coffee (or the headache appears), so I have to make sure it's very early, before a ride. Sometimes I have tea, which is a bit less strong. My morning "routine" is very regular, but since I started cycling, my motto has been "go early, go often." Some of it is nerves about starting any ride, but I also have an emergency supply of Pepto in my seat bag, or take a Zantac, to decrease acid.
I might try the probiotics, but it seems like I get a weird reaction every time I try some new mineral/vitamin.