I ate a paleo diet, which was basically just meat and vegetables, for a year and a half before this happened and I was the healthiest I had ever been in my life (high energy, 1-2 bms per day, good sleep, 6-pac, excema had gone, etc). It was only after the illness/medication that I had these problems. I am pretty sure the diet didn't cause it but as you mentioned it could be not helping me now. The thing is I have had high carb (fruits) low protein and fat diet whilst experimenting and it didn't change anything.
I have found 100g of triphala for £5. I figure I will use this in high doses of something like 20g a day (how much do you take btw?) and see what that does. If it does not work will try really high doses of something else that doesn't form dependencies.
You seemed to mention that once the constipation goes the bad bacteria will die down and good will grow in its place. Can you go into details.