No the GTS/GT stock STB will not fit with any intake other than stock. The Cobra/Explorer/GT40 intakes, and all aftermarket intakes, are taller than the stock intake. Maybe a box type upper on a stock lower would work if there is such a thing. But, I doubt it. Where the STB bar goes over the top of the stock intake is the problem. That's why, when you look at aftermarket STBs, you see the bar go around the front of the upper intake.