A 3-day stool sample sounds to me like they're looking for blood and maybe fat content. As long as you're taking samples, you might consider bacterial testing of one also. He could have a SIBO, small intestinal bacterial overgrowth. You may have to request this type of testing, however. (I had to ask three times before it was done because everybody was preoccupied with the idea of worms.)
There are a lot of things that your pup could have. Our Spencer, for instance, had intestinal malabsorption, SIBO, and finally IBD. I could go on forever about that but it might not even be relevant!
You're doing a great job of jumping on this problem! Let us know how things go. People here really do care.