It is best to start fresh... That said, keep the current HDD aside during the initial setup. Install the OS and drivers as needed.
Do you have an external HDD? I'd copy off the old HDD your User Folders (Desktop, Doc's, Music, ...) onto the External, IF you have saved game files you want to reintegrate, figure out where they are and copy them off as well, also know how to reintegrate them into the game once it is reloaded...
Reformat the old HDD. Now you can put the old HDD back in. IF you want to reassign the drive letters. My setup is C: - OS, D: - Storage, E: - BD-ROM g: - Games...
Now copy your User folders to a Folder on the reformatted HDD, call it Profile or something. Once copied off, goto your new user folder and use the Move function for these folders. Since the ones on the C:\Users\... are new, there should not be much in them.
NOTE******** I am not saying to move the whole Profile off the C:\Users\..., just the primary Data folders (Desktop, Documents, Downloads, Music, Videos, Saved Games) How to Explanation:
http://geekbeat.tv/redirecting-windows-user-profile-data-different-location/
Have fun... I also have an SSD just for Games...