This sounds like tritrichimonas to me. What kind of stool sample did the vet get? I'm guessing it wasn't a diarrhea PCR, which is what you really need. In reality you can test just for the tritrich, or tritrich and giardia (which would be my second guess) as that would be less expensive, but if they come back negative you're back to testing for everything else.
In the meantime, as the others have said, fenbendazole is a very safe and inexpensive medication that treats giardia and other things. Albon is also very safe and inexpensive and can treat coccidiosis (which would be my third guess), however neither of these will do any good if it is not what your kitty has. One thing that might help you get to the bottom of this faster if you already haven't done so, call your breeder and ask them if they have treated for any GI infections in their cats or kittens recently. If they have, ask them what cleared it up and start with that.