In my experience, watery stools are either caused by diet, parasites, a disease other than parasites, or stress. I assume the doctor has ruled out parasites.
If your cat was recently feral and it's diet, try wet food with some pumpkin for fiber. If your cat is outside or has access to small creatures, such as lizards, he may be eating them, at least in part. That can cause digestive problems.
If it's stress, try confining your cat to a room to get him accustomed to defending a small territory.
It'll be up to your vet to determine whether it's some other disease. Good luck!
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