I am far far from an expert but I have had a couple of weird air noises develop from time to time. (No, not me, My cars)
Could be that your throttle door is acting like a whistle when it is partially open. That single butterfly with the long straight edges could do it.
Are all the joints in your intake tube solid? Maybe one of them has a tiny gap.
Those double screws will whine very noticably even though the whipple is supposed to be one of the quiet ones. Maybe they quiet down under full pressure? I've never been near one thats working hard, they're always in somebody else's car and pretty far ahead by that time.
Dunno what the cause may be for your shriek but I've had them originate from the passenger seat, when it's occupied.

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Bone Stock '07 GT 4.6, Redfire w/ parchment leather, Automatic.
If it looks right, it is right, and I decide if it looks right. Paraphrasing Sir Sydney Camm (of Hawker aircraft IIRC)