Its most likely food related. im not 100% on gerd causing that much issue with bowels. What is your diet like? do you eat clean?
Try avoiding gluten, processed foods, dairy, and high fats for a week or two and see if there is any improvement. If you are eating foods that your body is either sensitive to or cant digest its going to make your BM all mucked up.
Try eating things like white meat chicken and turkey, either steamed or cooked in organic coconut oil. steamed veggies, and brown rice. You want to eat foods that are easy to digest. Also, add some foods that are high in prebiotics and probiotics. you can also take a probiotic supplement. As well as digestive enzymes.
Do this for a few weeks and see if you notice a difference.