4months old has mucusy poop for 8 weeks due to food allergy, i eliminated all possible food, still no better, will that permanently damage his bowel?

Food allergies?: First one needs to know whether the food allergies are clearly documented since your child may well have a malabsorption problem which may not be from food allergies. If you have indeed eliminated all possible food allergens, then the poop should have become normal in less than a week. Consult a pediatric gastroenterologist but may try a hydrolyzed protein formula for the time being.