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The scratching noise you indicated sounded like the arm that moves around to read data is f'ed up or possible making small scratches on the platters in it. The whining noise sounds like it could be a problem with the motor(s) that spin the platters. But from what you've been describing, I would recommend you back up your stuff and try reformatting. If it takes a long time to back up your stuff, so be it.
If the reformat and clean install doesn't help, the drive is close to being FUBAR. Only some thermite or a lightning strike could mess it up any more.
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- Master Shake
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