It was the JLT intake. Changed it out for a new one. Fixed. After all that shit. They changed the mold and made it more robust around the sealing points.
I now have a 2.6 Stage 1 Kenne Bell Kit and a set of heads. They came off of a buddy's car. (Popped @ 505 whp) Luckily the heads and blower didn't receive any damage.
My tuner says its back washing the air meter between 2700-3200 after that the graph smoothed out. Even at WOT it was doing it, it just wasn't noticeable driving it.
Defiantly not the tune. I took the car to another shop. He said they're may be a sticking tappet. Because when the oil is cold it runs like shit. As it warms it gets better. He said it was a valve train issue. Time to tear it down I guess. Damn it!