The vaccuum whistling is normal... and it's one of the primary reason why the stock intakes "are crap and restrictive".
Since the average person prefers a quiet car, car designers made intakes that also tried to muffle the vaccuum "whistling", hence the long stock intake and resonator box.
You've just experienced an engineering trade off. For freer flow, you gave up quietness.
Come to think of it though, a lot of the noise comes from the design of the intake and filter. It's effectively the "rough edges" which creates the turbulent air as it gets sucked in making that sound. If intake and filter makers would design a more horn like intake, that would probably help quiet the sound a bit....