The first thing I'd recommend is l-glutamine. It's great for both muscle recovery and gut healing... gotta love that. Get the pure powder, not capsules. It's tasteless and dissolves easily. I use Fitness Labs.
http://www.nutritionexpress.com/fitness+labs+l-glutamine+1+pound.aspx
I've had problems with all kinds of whey proteins. I use only isolate and have tried different brands and they all seem to bother me, but Proteins+ is the brand that was recommended to me by Jini Patel Thompson, author of Listen to Your Gut. It tastes great and has digestive enzymes added.
http://shop.genuinehealth.com/ProductSelection.aspx?Productid=2620&Categoryid=85
Currently, I'm using Healthy 'n Fit egg white protein and having better luck with it than the whey proteins. It also has enzymes added.
http://www.nutritionexpress.com/protein/egg+goats+milk+rice+hemp/egg+protein/healthy+n+fit+100+egg+protein+vanilla+ice+cream+2+pounds.aspx