Belle-
My kids have had similar patterns to yours. The three who took multiple years to sleep through the night all have issues with dairy- from mild intolerance to what we believe is real allergy. We are still waiting for our three year old to sleep through the night. She has gotten MUCH better since we took her off all dairy- including yogurt and butter, which people who are merely intolerant are supposed to be able to digest easily. I've always been a real butter user, so it's been hard to change my cooking to all vegetable oil based spreads. We have also switched to soymilk for cooking, whereas we used to make pancakes and such with cow's milk. I can see when she has a bit of cow's milk that ti does affect her at night- it can be just a single chocolate chip cookie, and then she'll wake 5-6 times crying at night and be difficult to comfort.
I believe that allergies can also cause or exacerbate reflux in infants. If you haven't checked out possible intolerances or allergies, maybe it could help.
