Just curious, but could you ask your vet if they checked the stool sample for coccidia? That was what initially caused really bad gas problems and somewhat loose stools in my kitten Lily. She improved a lot after that was treated, but apparently has a sensitive stomach as she has continuing issues. I experimented with her food and Cal Nat chicken and Nutro both work well for her, Cal Nat a bit better, probably the simplistic formula. Hopefully it will work for you, it does take time for the gut to settle down. Also, whenever I switch foods (slowly, of course) I have to mix Benebac into her canned food, otherwise she has really bad gas problems again.
I've found Benebac at pet stores, but I like the dial-a-dose version I got from the vet a lot better. It's easier to handle that way.