very likely a local minima/maxima of resonance causing back pressure in exhaust flow and up through the intake. the StainTune may have it there. the factory likely has it somewhere else. I play with inserting the silencer (outlet reduction) and find the torque is smoothed out. I suspect it fills in that trough.
for offroad, I use the black 'n' blusaberg. the GS is simply too big - even though I'm not exactly small at 6'6" and 250 lbs. the 'berg has 3 fuel injection maps. the softest map has the best power delivery for tight trails. the upper two maps are much different and carry a bigger power hit. it has the stock pipe which flows fine and has the advantage of stealth. the only thing you hear is the honk of the airbox - located right between your legs.