Don't let Bleepingcomputer scare you from using Combofix. I have used it many times to clean computers when all other AV programs have failed to do so, and have not had to re-install any system files after using it.
Before it cleans your computer, if not already installed, it will install the Microsoft repair console, create a restore point, and backup your registry. After it has cleaned your computer it generates a log file, just like Malawarebytes Anti-malware does, for you to read. You do not have to do anything else but reboot.
Combofix is not a cure-all. What I have found is that it is able to run when other AV programs can not install, even after changing their exec names and running in Safe Mode, and will find and delete those viruses causing this. You can then install other AV programs, like Malawarebytes Anti-malware, SuperAntiSpyware, Hit-man Pro, etc., to clean up those viruses that Combofix misses.
As Chiefcrowe suggested, you can also try the bootcd AV programs like the Avira AntiVir Rescue System. http://www.free-av.com/en/products/12/avira_antivir_rescue_system.html
I have had limited success with these. They don't seem to dig deep enough, and only delete a fraction of the viruses on computers I have tried them on. That may be enough though to get your computer to boot up, or be able to install other AV programs.
And we are back to the question of whether the computer is 100% virus free, and should you do a complete re-install of the OS. I read a statistic that 80% of the computers in the US are infected. Are you 100% sure that the computer you are reading this on is virus free?