first of all: Buy a new harddrive, preferably the same size (even more preferable, the same type) as the on you have now. Then get a program to do a sector-by-sector clone of the harddrive. I think there's one of these on the Ultimate Boot CD ubcd.sourceforge.net . Not sure though. Anyway, clone the drive, use the clone, see if that helps. If it doesn't, you'll have a nice backup. I'm not sure if there's any way you can repair the NTFS table without completely reformatting (never done it. Never had to in 3 years as a data recovery tech). At that point, if it's not a harddrive issue, I'd reformat on the original drive, and use Command Prompt to copy the folders over, and use Files and Settings Transfer Wizard (works unbelievably well for a MS program). I'm not exactly sure how to do this on a harddrive that's in the computer you're working on. If you can't, go to your original harddrive and export the ENTIRE registry, merge it to your new install, and just copy all the files straight over via cmd prompt. There's even a program out on the web, called xxcopy, that lets you ignore copy errors, so one single error doesn't make you recopy ALL of your files, the way windows does. Don't use the clone again, because if it is a problem with the NTFS tables, you'll just be cloning the problem all over again.
That's what I'd do anyway. If you like, though, there's a program that MAY be able to do what you're thinking of.