This thread is a little confusing, but I get the impression that he has never messed with the tune, and found out it has a stock tune. So when he got the car, it had a stock tune with those mods on it. Then he drove it with the mods and stock tune for 6 months until he put the stock stuff back on.
So OP, what these guys are trying to tell you is that you drove your car with an improper tune. Depending on what tune your running, you were either messing the car up when you got it, or you are now that you put the stock stuff on it.
With the mods you have listed, that car should have been running a stage 2 tune when you bought it.