Rest well
What was the result of the second scan after disabling system restore? If the scan was clean, then that's progress. If it found it again, and it were me, I would just wipe and restore.
The article Jeff posted is interesting to me, but pretty intricate and following it's many steps may take just as long as doing a complete reformat of the hard disk, and re-installation of the OS, drivers, software, data, etc. However, that is just my opinion. Note that I know where my data is located, when it was last backed up, where my installation media is located, what hardware drivers I need, and how to do it all within a day.
I have used BartPE in the past to gain access to an NTFS formatted primary boot partition for particular situations like backing up data that I would otherwise loose when I reformat the disk. I never though about using it to replace certain files on the boot partition, which is what I find interesting in that article. If you can copy the data to other media (like a USB hard disk), and you have all the installation disks, then I would forgo attempting another repair.
If you still want to try to fix it, I'm willing to kibitz as long as you're willing to exercise.