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Yes, you need to boot the CD or flash stick to run the full scan with MS System Sweeper to disinfect.
Then you need to boot the Win7 DVD or Repair CD.
If you are booting them and they still stall, test your HD using maker's diagnostics/repair CD extended scan: HD Diagnostic
Next test your RAM with memtest for 5-6 passes: RAM - Test with Memtest86+
If these fail try resetting the CMOS: Clear CMOS - 3 Ways to Clear the CMOS - Reset BIOS
While in BIOS setup set the CD/DVD drive to boot first, followed by HD. How to Boot your Computer from a Bootable CD or DVD - Boot to CD
Now try booting the scan CD and Repair CD again. Look for the prompt to "Press any Key to boot CD." If it fails reboot and tap the F key given on first boot screen for Boot Menu, select CD drive to boot.