System files not available

I have a compaq pressario AMD athalon, 128 ram, Millenium edition. I found I had tons of sypware trojans that disabled my Norton Antivirus. I downloaded AVG which cleared them up with spybot too. It must have messed my system files up too as I can't view the control panel files or files under C drive. It shows the #of them listed on the bottom, but can't view. I think I might have to do CD Restore to wipe out hard drive and start over, but I want to save my files first, which I can't do since I can't access the folder they are in. I didn't do backups lately to do that. It also made a conflict with WMP version 9, which shows there is a confilct. I am able to use NERO brand player that I just downloaded so I'm thinking it is a microsoft problem. Any help would be appreciated for this new forum reader.