I'm not metmom, but I'd like to add my experience.
My husband and I both have seasonal allergies and my older son (breastfed for most of 6 months, but not exclusively- he got formula at 6 weeks and cereal also at 6 weeks in an effort to get him to sleep) was allergic to milk and suffered from eczema and numerous ear infections as a baby. By 3 years old he had asthma.
When I got pregnant the second time, I had read enough about allergies to believe it seemed reasonable to at least try to breastfeed exclusively for 6 months. The hardest thing about it was resisting pressure from my in laws. Luckily they didn't live nearby!
My second son is healthier in every measure than my first. But the two children are very different in almost every respect, so it may not have been the breastfeeding. I'm glad I did it. It wasn't as hard as I thought it would be. I would definitely consider it if there is a family history of allergies.
About a year before I had my first, I ran across an article in Science News magazine (that would be about 1987 sometime), that stated that alternating feedings of breast milk and formula may actually cause worse allergies than just formula feeding. There's something about changing from one to the other within a short period of time that the babies system cannot tolerate. IIRC, it puts a strain on their digestive tract to constantly have to adjust to digesting different kinds of substances. Even a few weeks of breastfeeding can be beneficial. I know some people can't manage it but even to do it a little before switching over helps.
I know of a kid who has the absolute worst food allergies I've ever known (anaphylactic shock) and his mother did this and is blaming herself now.
My son, who was breastfed a long time, had problems with ear infections for one year, also. We don't know what caused it.
I had the same problem with my m-i-l about breastfeeding. I was also glad they lived further away.
Your story sounds exactly like mine, except I was able to figure out somewhat early on in my oldest child's infancy that the cow's dairy products I was taking in were coming through MY milk. My oldest child was MISERABLE until my system cleared itself of the dairy intake - takes up to 2 whole weeks. And then - WHAM - she started sleeping through the night - thank goodness because I was totally sleep-deprived until then due to her crankiness and colickyness and crying/screaming fits.