DS and I have been practicing EC since 1M and so I don't miss a thing when it comes to catching poop symptoms of food allergies. Yes. Mucous is a symptom as is foamy poop, blood spotting, etc. I have had to eliminate dairy, wheat, gluten, soy, tomato, YEAST, cane sugar, egg whites and blueberries. I discovered most of these through elimination dieting but had them recently confirmed by an ELISA blood test (drawn from me - Mom's antibodies are the same as Baby's). I also had a stool sample from DS. I learned a lot from that. He doesn't have enough good bacteria and has an overgrowth of Klebsiella. I think that when I started teaching him swimming in the pool at 4 months is when the good bacteria in his gut were compromised. I am giving him a probiotic and some Nordic Naturals cod liver oil now in a tiny bit of applesauce while I follow the Body Ecology diet and research colon care, digestion, and food allergies.
This is all probably more than you wanted to hear but maybe it will give you some ideas... read a little about elimination diets (Baby Matters is a good book), watch out for chlorine, consider an allergen-free probiotic, Body Ecology is a great diet as is the cd "Understanding the Leaky Gut".