C_Mac23,
It could also be a problem with food combining, which if done improperly can really wreck havoc. I know because now that I follow it strictly I see the huge difference. Here's a good link for info: http://cureforulcerativecolitis.com/step-1-methodology-to-eating
As far as a good protein drink: actually the safest one IMO because you're not sure if you might be intolerant of lactose, casein, etc... would be Pea Protein or even Hemp Protein - I know Dr. Mercola makes a very good quality Pea Protein liquid, but you can probably go to your local health store and pick some up.
Make sure you read the labels carefully to make sure it does NOT contain any dairy, gluten, wheat, high fructose corn syrup. I would mix it with Almond Milk.
It's good that eggs agree with you. I found that I could tolerate egg yolks, but not egg whites.
I am hoping that cutting out everything and only trying a few things at a time will help the food journal be more effectice.
Yes, that will make it easier to make the connections in your food journal. But don't forget about the food combining as well.
Let me know how you make out.