Even a move to Jardine headers (which are (I accept) far from perfect) improve flow - it's a tangible difference. Proper headers ( and I like the sexy curvy look more) will certainly improve things.
One point that's not been mentioned. Whilst pipe effective length affects WHERE max torque is delivered - the Volume of the system affects how wide that band of torque is.
Shorties will almost always make the amount of torque FEEL more tangible because it's a peaky-er curve.
I have THUGS fitted on the end of Jardine headers - these flow well but are a bit short.
Fortunately though they are torque-y right where I generally ride - rpm wise. They'd be better a bit faster (more rpms) - but then my licence would be at severe risk.