Hi,
how do you know files are missing? Error messages or?
Have you tried system restore and go back to a point before the files were lost?
If you have a windows 8 disk you could change the boot order so the system boots from the disk. Boot from the disk and instead of re-installing click repair. The repair button is on the same page as the install button so you will have to go through the disk as if your actually doing a clean install.