Huge Problems with XP Pro Install

Hello- I had a trojan get a hold of my pc, avast! caught it and put it in the chest. Shortly there after, XP Pro wouldn't start. We got a black screen saying that '\Windows\System\Config\Sys' was either corrupt or missing and to do a 'repair' with the XP CD. All that did was take me to the Recovery Console.
So, I wiped a 160GB Barracuda I had laying around (used to be a fast drive) and did a clean install of XP Pro. After doing this, my Video Card quit and I am running off the integrated Intel graphics now. On my new install, I am the Administrator.
Here are the problems- 1) Windows takes forever to boot, the Desk top icons take a long time to load, and even the browser, when clicking on the quick start icon on task bar takes a while to pop up. 2) When I go into 'msconfig' from Start>Run, unchecking start up items and applying brings up a Access Denied error stating that I must have administrator privileges, or something to that effect.
No, I don't have an HP printer. I have an Epson and have never had a problem like this before. We have not found any solutions via Google search.
Could someone here please help me get my pc running clean and back up to speed?... I would appreciate it.
Furthermore, I don't think the integrated graphics theme has anything to do with it. I did pick up a half of a GB of RAM by removing the card. I have 4GB's installed and 3.11GB showing in Device Manager.
Again, Thanks!

 

A few things to check. Since your graphics card failed to work after the re-install I suspect your chipset drivers might be FUBAR. Have you checked in Device Manager for any issues? Also in Device Manager expand System Devices and check what is displayed there. If your specific chipset isn't listed then you need to install drivers for it.

Download the manufacturer drivers for the chipset your board has, and see if that corrects your issues.