Personally, I would wipe the drive and reinstall Windows 7 SP1. If this was an OEM and you cloned the drive you might be able to set it back to a factory state if there was a factory reset partition intact.
At any rate, I would back up your Activation Files using Advanced Tokens Manager. Download the program and unzip the file to a folder on your Windows 7 desktop. Run the program. You will see a key listed. Write that down for your install. Click Activation Backup and when completed the button will show as Activation Restore. Save the unzipped folder on the desktop to a flash drive. One you install Windows 7 copy the folder from the USB flash drive to the desktop of the new install. Click Activation Restore. No need to activate through Microsoft servers or use phone activation. This is only if you do not have a retail key for install.
Once you have a clean install, updates downloaded, and programs installed I would create a complete disk image to a USB external drive using one of the following programs. All allow you to create rescue media in the form of a DVD or USB flash drive. This allows you to restore the image on the USB external should the computer no longer boot to file system corruption or a failed drive. You are not cloning but creating a disk image. Multiple images can be backed up to the external drive. If your drive failed, boot the rescue media and restore the image from the USB external to the new drive. You would be back up in minutes with all updates, programs, and settings intact.
Macrium Reflect Free
Aomei Backupper Standard
Easeus Todo Backup