Reload of Windows XP Pro after virus

Hey all. Got a Windows XP Pro computer and got a virus some time ago. Virus was cleared but the OS is not doing so well. So I decided that I am going to reload Windows on a seperate disk and then transfer my files from the old installation to the new installation. It was a RootKit Virus and it was cleared, using TDSSKiller and ComboFix.

The older version of the installation is running OK but my administrative priviledges are now limited and I can't change them, even if I create a new user with administrative priviledges. Did this with the user windows default administrator in safe mode but even the new user had no priviledges. As an example, if I try to change the startup using msconfig, when I change a value I get an error message stating that administrative priviledges are needed. The file never changes so if I hve to change the boot.ini file, I had to do it in DOS. Same thing happens if I try to do it through the control panel.

So to be safe, I am just going to do the re-installation. Will my McAfee virus program catch any personal files that I send over? I plan to transfer them to a portable disk and then have McAfee scan the disk as it comes online using the USB port. I do not want to transfer the virus over even if it is supposedly eradicated. Still have some quarentine files that I want to get rid of too.