Got back from the vet. They don't feel anything is wrong with Mac. And it's mostly normal puppy related stuff plus the stresses of coming home to us, diet change, etc...
However they did prescribe some probiotics and an antibiotic called metronidazole to kill the bad stuff and restore a normal flora balance in Mac's tummy.
We did return the Wellness large breed puppy dog food for natural balance sweet potato and fish formula. I decided on this after talking with a gal I work with about her Great Danes and their food issues, she's had really good luck with this formula. After reading many mastiffs have chicken sensitivities I really didn't want to risk it.
We started to mix in the kibble with the rice/elk and will slowly switch him over to straight kibble.