Thanks everyone. The thing about worms that I learned is the meds kill the worms but not the eggs, so they typically need to be deformed a few times to get rid of them. He was deformed by the breeders vet and will get deformed 2 more times when he goes in for vaccines.
The vet checked him really well for fleas ... Used 3 different methods and couldn't find anything.
He is feeling back to his normal self this afternoon and evening. He still has runny poops, but it's after meals now instead of every 20 mins like it was overnight.