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windows\system32\config\system missing or corrupt

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New user, sorry if problem has been posted before.

Dell 4600c desktop
WinXP Home
P4 2.8 GHz, 512 mb RAM

I may have made the mistake of trying to help a friend with what appears to be the family computer. It was her impression that spyware, and lots of it, was the only problem. I took it home yesterday and rolled up my sleeves:

Spyware/Virus Removal Action Taken
Spywareblaster: loaded and updated
Spybot Search & Destroy: 200 items identified and removed, including files to disable Windows Firewall and Update Notification.
Ad-aware: initially kept shutting down system. After some research, I installed the VundoFix, and then it worked fine. 114 objects detected and deleted
AVG: 41 files infected, all healed

I then used RegCleaner and RegScrubXp to clean out the registry:
RegCleaner: ~15 items identified and removed.
RegScrubXP: ~165 items identified and removed.

Everything shut down fine and I went to bed feeling like I had accomplished something good. However, this morning the system would not boot and displayed the following message:

Windows could not start because the following file is missing or corrupt:

After doing some more research, I identified 2 options: do a repair operation using the WinXP CD; or remove the hard drive, install it as a second drive in a working system, and copy the following files from the Windows/Repair folder (default, system, software, sam, & security) to the Windows/System32/Config folder.

Since the WinXP CD is not available, I chose the second option. Not being hardware savvy, I was surprised that I could get the hard drive installed and recognized in my old PC on the first try. I was then able to copy those files from the Repair folder but I had to create a Config folder in System32 as there was none there. After that, I re-installed the hard drive in the original computer and was able to boot up to the desktop. That’s the good news...I think.

The bad news is that the overall look seems to be like everything was reset. All Programs show up in the Start Menu, but not all of them will start. It also appears that no actual files were erased...PHEW! Other observations include:

*nothing in system tray except for the clock
*only 1 item listed in msconfig: mstinit.exe/firstlogon
*480x640 screen resolution, cannot adjust in Display/Settings tab
*no more Windows logon password

The Device Mgr also has a yellow ? next to the following “Other Devices”
Ethernet Controller
Multimedia Controller
PCI Simple Communications Controller
SM Bus Controller
Video Controller (VGA Compatible)

Can anyone enlighten me as to what I just did and how I can best move forward? All input is greatly appreciated. Thanks!
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