I'm sorry to hear that you had stomach flu and other problems. I hope you can take comfort in my telling you that my recovery made a substantial leap at about six months, and things kept on improving until 12 months.
Like Winterberry said, it's likely that your j-pouch will continue to improve. As you had a setback early on, maybe you will notice improvements coming a little later.
I found that taking smooth Metamucil (psyllium husk fibre) just before all main meals helped me a lot. I take a generous heaped teaspoon mixed with a small amount of water and gulp it down quickly right before eating – like 20 seconds before. You have to swallow it quickly before it turns to jelly!
I remember having that uncomfortable feeling between BMs too. With time and Metamucil and watching my diet, it definitely improved.