Hi Brooke-
Is the poop either greenish or yellowish? Have you wormed him recently? Both Giardia and Coccidia are common in puppies. And both of these conditions need to have a special fecal test to detect them. Unfortunately my dogs have had both when they were puppies. Giardia can be intermittent and hard to treat. I would lean toward testing again. Also check out this site for help with diarrhea. It has a lot of helpful information in my opinion. http://www.dogaware.com
Click on digestive disorders tab. My pups did best on grain free Victor when we were battling this issue and are doing well on Whole Earth Farms now. It is very easy to digest and I think it is actually ok for large breed puppies. Good luck. Been there and it’s frustrating!
