I agree with Mike J that it sounds like your throwout bearing, but it's odd that the noise is still there after putting in a new one. It's too bad it's such a PITA to change them since they're so cheap. When it was apart was the throwout arm pivot inspected? If the pivot is badly worn, it can make the throwout bearing come up on an angle, rather than straight in.
I have also heard worn pilot busings make noise, but not a whistle/whine noise.
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