I'm sorry you're still feeling sick. You are probably not getting CC if your TTG has dropped back to normal. What your Dr. probably didn't tell you is that a Marsh 3 biopsy typically takes a couple years to heal, and can take as long as five years if the damage is really bad. At three months with the TTG down, now your body can start to repair damage.
I also had to go casein-free/soy-free when I first got off gluten to be rid of the stomach trouble. I could only digest those foods after about a year gluten-free. You might try eliminating some of the common problem foods like dairy, soy, and corn to see if any of those are making you feel ill from non-celiac intolerances.
That's what I was going to say!