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Try booting up in safe mode and see if that makes a difference. Also do your spyware/adware/virus checking when in safe mode to get everything. Also defrag your disk like vinaur says. When you're just at your desktop, hit CTRL-ALT-DEL and see what processes are running, see if anything other than the System Idle Process is running high. If you're just at your desktop the Idle process should be up to 99% or so. Is anything else running high?
I would recommend formatting the disk and re-installing Windows but if your files are taking that long to transfer it might take a month. Also when they say they reseated the hard disk it just means making sure it's screwed in properly and the cables are plugged in nice and tight.
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