Follow your instincts on the milk allergy - my son had "reflux" and was going to be started on prescription meds until I asked our ped whether there'd be any harm to doing an "elimination/addition diet" to find out whether any foods could be causing the problem. Well, wouldn't you know it... within 5 days of removing ALL cow's milk products from our son's diet, he was a different child - and because I was breastfeeding, I removed all cow's milk from my diet too. Worked like a charm, no prescription meds necessary (these would NOT have treated the root cause of the problem, in our case, it would have only addressed a symptom yet my poor kid and his immune system would have still been reacting to the allergen!), and we are ALL healthier for it.
Since having gone through this with my own baby, I've met quite a few other breastfeeding moms who have had similar experiences - although instead of reacting to milk, perhaps their child was reacting to gluten, or eggs, etc. Even allergy testing wasn't reliable for figuring out the cause, in many cases. Only eliminating foods until the symptoms went away (an obvious decrease or disappearing of reflux, diarrhea, skin issues like eczema, sometimes even sleep problems!) and then adding a food back in (ONE AT A TIME ONLY!) and watching for potential reactions to crop back up over the following 72 hours -- this was, for many, the only reliable way of figuring out what was truly the cause of our baby's relflux and/or skin issues and/or bowel troubles and/or sleep issues. Once removing the food(s) that was causing the problem, our kids became obviously better.
If you do wish to pursue allergy as a possible contributing factor (and I highly encourage you to do so --> kids w/ reflux or GERD are MUCH more likely to have food allergies), here are a few resources that I found helpful:
Kellymom (evidence-based breastfeeding site) has a page on breastfeeding a baby who might have food sensitivities or allergies:
http://www.kellymom.com/babyconcerns/food-sensitivity.html
Email list for moms breastfeeding babies + toddlers w/ food allergies - excellent support for doing elimination/addition diets, lots of collective experience/wisdom here:
http://health.groups.yahoo.com/group/foodlab/
Dr. Sears has a great page on tracking down food allergies - the chart is excellent and really covers a wide range of the lesser-recognized symptoms of food allergies:
http://askdrsears.com/html/4/t041800.asp
And at your local library, check out Dr. Doris Rapp's book called "Is This Your Child?" - here are some of the reviews from Amazon:
http://www.amazon.com/review/product/0688119077/ref=dp_to...
Last but not least, I've heard good things about but have no 1st hand experience with this blood test for allergies:
http://www.alcat.com/
Best of luck, and definitely follow your instincts -- food allergies are often grossly unrecognised or completely misdiagnosed (as reflux, GERD, chronic ear infections that require tubes, etc.). There's a lot of great information and support out there if we're willing to do our own research. I love my pediatrician for many things, but I've found that my pediatric group (and even ped specialists like our ped allergist and ped gastro) has not been very on top of things when it comes to accurate information on infant and child nutrition -- I've received less-than-stellar information and diagnoses when it comes to breastfeeding and food allergies. I'm glad I trusted my instincts, did my own research, and sought 2nd and 3rd opinions when needed. I've since met many other mothers who have had similar experiences, so listen to that mothering instinct! :) Hope you're able to pinpoint the cause(s) and find some relief for your daughter (and yourself!) soon.