Use the system install CD or backup.
When prompted which partition to install to, select Repair instead of installing to the partition.
After the repair, you will have to reinstall most the Windows updates again. Drivers will still be installed, and none of your data will be lost, which is some good news for you. The constant reboot after a few updates will be the common Windows user experience.
Do a scan disk, defrag, registry clean, and you should be set for your Windows to continue to operate normally.
