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Are the stools normal otherwise?
No blood? solid? Not too hard or too soft?
What type of food are you feeding?
One thing I would like for you to do is having at least one more stool sample checked on him. There are protozoan infections like giardia and coccidia that can be difficult to find under the microscope in a vets office mostly because these are shed at different intervals. One can be negative one day and then positive the next. You might even ask the vet to consider sending home a wormer called Albon and Flagyl for the loose stools to see if this corrects the problem. I believe it will with him being a stray at one time this is very likely an issue.
The other issue you have here is that kitten food in an adult cat can cause some intestinal problems including the loose stools and since this is such a dramatic change from what he used to be eating birds, mice, etc it can take some time for his digestive tract to adjust to it. Since you are not seeing his ribs as well anymore you might just want to switch him over to adult food now because cats who are indoors can plump up rather quickly anyway.
One other thing you can do to help is add some plain uncultured yogurt to his food once a day. This will help to replace the bacterial flora to his gut and MAY improve the consistency of his stools.
The simpliest issue to rule out would be the coccidia. However, one condition that can cause these soft serve stools is hyperthyroidism. Other symptoms you may notice is an increase in appetite and weight loss. If you are up for it you might want to consider testing for this. Liver disease also causes soft stools but in most cases when you are to this point you will also notice jaundice, no appetite and vomiting. Diarrhea is unlikely in kidney disease.