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No, the bad sectors won't transfer, but any information stored in the bad sectors won't come over, possibly causing file system or OS problems. I've never had any luck with cloning utilities from a bad drive anyway.
The controller card would have been a better way to go because it doesn't require the EZ-Bios overlay, but if you have it up and running now, I'd leave it alone till you build a new system - which won't need a controller card.
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