Oh, how I feel for you! My daughter was a preemie, so we were that much more obsessed with her nutrition and weight gain. At about 6-weeks-old she started projectile vomiting. We tried Zantac, then Prevacid. Neither helped, and her reflux just got worse with blood in it. It was terrifying. Each time she would nurse, she would throw up, so then she wouldn't want to nurse and my milk supply went down. Her doctor said that if it was just reflux, the meds would have helped and that there must be another irritant in her stomach, so had me stop eating all dairy and soy. It was so hard, I was always starving but having a hard time finding things to eat (if you read ingredients, almost all food has some dairy or soy products in them!). I was taking fenugreek and trying to pump frequently, but my milk was still low. When I finally figured out some meals for me and ate more, it definitely helped my milk supply. My daughter's pediatrician said that it could take up to 8 weeks to get all of the dairy out of my system. During those 8 weeks we would keep her upright 24/7, sleeping with her on our chests on the couch in sitting. I took her to Children's hospital and had a custom foam wedge made for her - it was about 50 degrees and had bolsters and velcro straps - the works! It truly did take about 8 weeks though of me off dairy for her to get excited about eating/nursing and for us to be able to put her to bed in her wedge. I think she really did understand that nursing made her stomach hurt, so didn't want to nurse. I ended up back eating soy when she was 4 months old, but stayed off dairy the whole year I nursed her. I had to be incredibly aware of what I ate to make sure it had NO DAIRY! Even foods with nonfat dry milk would seem to upset her stomach. I tried the hypoallergenic formula to supplement her diet (Nutramagin), but she refused it. I couldn't blame her - it smelled so bad!! Plus, then when she would spit up, it smelled even worse!
Good luck! I would really recommend avoiding dairy and looking into getting a wedge made for your daughter. That combination really helped us! She is now almost 19 months old and tolerates cheese and yogurt just fine. She still drinks soy milk, but I'm hoping to transition to whole milk soon.