I've had similar on an older 'bike. An older and wiser head told me it could be air leaking into the exhaust where the pipe went into the head. I re-made the joint with exhaust paste and it cured the problem.

I couldn't figure out how it would make a difference, nor how air could leak in without any evidence of exhaust blowing out.

The aftermarket header pipes maybe need sealing with high-temp RTV where they meet the exhaust gasket. If that doesn't cure it, it's also possible the aftermarket headers have a slightly different (larger) internal diameter to the factory originals. Original headers are often double-skinned (smaller ID), and I suspect the stainless replacements are not.

The different ID will alter the fuel/air mix a little, especially in high-vacuum situations such as on the overrun or steady light throttle. You might be able to dial out the problem by playing with the pilot screw setting. Manuals will usually give a pilot screw setting with a range of plus or minus a quarter of a turn. Whichever is the richer direction for your pilot screws, try half a turn in the richer direction and see if it improves things.