It is very hard to advise you in regards to your diet. The reality is, there is a lot of highly processed food in your diet. The only protein sources you eat are processed. The primal way is unprocessed foods and low toxins. What about homemade bone stocks and soups? They are highly nutritious and good for the gut.
Maybe a little more info would help.
What is your current weight?
Do you have a copy of your last thyroid labs? Many people are not properly treated for thyroid disease even after diagnosis.
What do you mean when you say things irritate your gut?
Do you have other symptoms?