Sounds like he may have some sort of intestinal parasite like Coccidia or Giardia---both these make foul-smelling poos. When you take him in to vet to be checked out bring a fresh stool sample with you for the vet to test. Hope you soon are able to find out what the problem is.
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"We humans are indeed fortunate if we happen to be chosen to be owned by a cat." -- Anonymous
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