Questions About Enfamil Nutramigen

On Monday, my 4 month old daughter was diagnosed with cow's milk protein sensitivity. I had been nursing, pumping, and supplementing with formula, but now I'm thinking I'm going to switch entirely to formula, and the pediatrician had recommended Enfamil Nutramigen. She's been on it a few days now, and her poops have changed in consistency, frequency, and color and she has developed very bad diaper rash, which has never been an issue before. Did anyone else's little one experience this when starting this formula? Will it go away? How long should I give it before switching to Similac Alimentum? Has anyone tried both? What are the pros and cons of each? TIA!