I am so sorry your baby is not feeling well.
There are many possibilities so I will try to cover everything.
He could have coccidia or giardia,even if he tested negative. I will expain why.
These protozoan parasites run rampant in shelters and pet stores and catteries They are very common in cats .Most are born with them.Many cats harbor them without isues until the immune system weakens,
Metronidazole (flagyl) is scripted for these parasites. It must be given for ten straight days - the off a week and repeat another ten days.That is because the parasites shed cysts (eggs) that do not mature in a week hence the cat keeps becoming reinfected.
Because of this lack of shedding into every stool, THREE separate tests are required to rule it out.
Of course stress is a factor.It allows opportunistic bacteria to take over.
He may just have bad bacteria.
Give him one half teaspoon of plain yogurt every day. The acidophilus will keep "good" bacteria in his colon.If it is not strong enough get acidophilis for cats at a human health food store.It will firm the stool in only four doses (days).
If he gets dehydrated and hypoglycemic due to diarrhea - First put a drop of pancake syrup on his tongue to raise his blood sugar.
Next, begin by giving him two droppers (cc size) of unflavored pedialyte every ten minutes for an hour. Next water baby food chicken or turkey with no onion or garlic and give only one dropper every ten minutes for another hour. Wait two hours and repeat both. When he feels hydrated he will lick up the gruel on his own.Add one tsp of infant rice cereal to a can of wet food at each meal.
Make a temp electrolytes solution by adding an eighth of a tsp each of salt, sugar and pancake syrup to 12 oz of water.
To cure diarrhea:In review:
Boil two ounces of milk - cool to room temp and give him one ounce.
Add cooked white rice or baby rice cereal to his food.
Cats cannot take any human OTC's because they are sensitive to the ingredients so we have to treat him holistically.Yes antibiotics can cause diarrhea but flagyl usually cures it not makes it worse.
Please let me know how Cookie is feeling. If you have any questions along the way, I will be always be here for you.
I hope your baby feels better very soon.
Warmest best wishes,