The stock airbox setup (albeit the revup version) is known to be the best for power due to the design and ability to keep heat soak at bay, the aftermarket unit you have on has no heat shield so will draw a lot of hot air in from the engine bay.
The HKS is a dry filter meaning in contains no oil like its rivals k&n etc so won't cause any possible issues with the mass air flow sensor being contaminated with oil, usually happens when the filters are cleaned and too much oil is put on.
Hope that helps