Hi there! Welcome to the forum! First things first, the Science Diet has got to go! And the fancy feast as well. A limited ingredient diet is really the way to go now using something like duck and potato to go easy on his stomach
Chicken By-Product Meal, Whole Grain Corn, Corn Gluten Meal, Animal Fat (preserved with mixed tocopherols and citric acid), Brewers Rice, Chicken Liver Flavor, Fish Oil, Flaxseed, Dried Egg Product, Soybean Mill Run,
Random chicken parts, tons of corn and soybean scraps would be enough to make anyones tummy hurt
Secondly, a more intense round of deworming would be what I would do. Legally I can't prescribe anything for you of course, but if this were a shelter animal I can tell you he would be put on Albon, Panacur and probably Metronidazole as far as prescription medications go. I would ask my veterinarian about these medications to see what they had to say.
Cats can have IBS and other digestive disorders, but it is far more likely this is a dietary issue or a bacterial infection. I see that you say the stool sample was checked, but sometimes Coccidia can be overlooked. It's ova are very tiny and often look like air bubbles. I often overlook them on fecals (hence why I never volunteer to do them!). Albon is the treatment you need for this.
I hope some other members can chime in with some ideas, but if this were my pet the route I would take is changing the diet to something simple and doing a round of extremely safe broad spectrum medications just to kill anything off that could be hiding.
And congrats on the new kitten!