I suppose anytime some mentions "cloning" in reference to Windows 7, I immediately get a little nervous.
Are you showing the same drive letters as the old system, like is C: still the OS partition?
Is there some reason you did not just image the drive with the Windows 7 Backup and Restore utility then restore that image to the new drive?
If you are going to keep your current configuration, perhaps disassociating the SSD or setting it to available might allow you to reconfigure the array with the new drive.