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.
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.
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.