Bf 3 mo old with cow milk protein allergy. Dairy free x4 wk, minimal soy intake. Symptoms improved but not resolved. Normal weight gain. What do I do next?

Continue avoid milk. It takes time, so a continued milk an dairy elimination diet is in order. It would be important to read labels to make sure there is no "hidden" dairy in other foods. Also, there may be another food allergy besides milk. An allergist can assist in the search for the cause.
Consider other cause. Consider other diagnoses: lactose intolerance, food allergies, colic, gerd. Bifidobacteria and lactobacilli has been found in infants fed with whey formula. Oral probiotic supplementation can reduce the prevalence of atopic disease by stabilizing intestinal integrity, increasing numbers of specific intestinal flora & reducing inflammation, choose formulas that increased the number of these bacteria.