You typically see the whining issue when you install an after market amplifier and create a "ground loop" (Google the term to learn more). Go back to your grounds and reground them or if you cut any wires on the amp inspect them. You can use a ground loop eliminator that plugs into RCA inputs on the amp but I'm not sure how it works with the stock amp. I had the issue and moving my grounds helped but didn't eliminate the problem until I installed the ground loop eliminator.
Have you done anything with the stock amp?
-Steve
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2001 Boxster S
Desnorkled
Pioneer Avic D3
JL Audio 6.5 inch subs (in the door)
Pyramid 4 channel amp
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