Making him poke his head our of his shell means the preacher was being more relaxed and open - less guarded than usual. It comes from animals like tortoises, which go into their shells when they're scared and come out of their shells when they're more relaxed or confident. A stray dog is a dog without owners. It is the same as saying a street dog. He's a stray if ever I've seen one means the dog is really obviously a street dog. [If this dog isn't a stray, then I have never seen a stray before.]

‎"He was making him poke his head out of his shell." - He is breaking off from the usual him. For example, he used to hate dogs but Winn-Dixie made him "like" dogs for some reason. The book even mentioned " Winn-Dixie was having a good effect on the preacher." "He’s a stray if ever I’ve seen one." - Since he is referring to a dog, for me it means "no owner".