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Its the head unit more than likely.
Pull the unit out. Take the ground right off the harness of the radio (not the adapter plug) and put it to bolt in the center console.
If that doesnt seem to fix it take another set of RCAs and just run them above the carpet to test if its the RCAs picking up noise. I highly doubt the rcas since you are getting alternator whine.
Lastly your alternator might be on its way out.
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-Ryan
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