You could try TDSSKiller, which might fix some of the problems.
However, rootkits are deep infections which can either write a hidden boot sector or compromise OS files. And, rootkits tend to introduce other viruses to the system. Some rootkits are able to circumvent AV scans. The Sirefef virus does this by presenting a ligitimate file to the AV scanner. When an AV scan is run, the legitimate file is presented to the scanner and it comes back as clean. In reality, once the legitimate file is run, the OS switches to the rouge driver
and the rootkit is active and running. The Microsoft site recommends a clean reinstall for most variants of rootkits.
Being that your initial scan showed multiple infected files, the best/safest choice is a clean install.
Also, note that your AV scanner was denied access to these files, hence, no action was taken to remove them. Also, don't you find it strange that despite the detection of multiple infected files to which no access was allowed by the AV, they disappeared during the second scan? This is typical of the latest virus strains adaptive behavior.
Yes, viruses will jump to USB & removable media drives.
You could have been infected in multiple ways, a compromised website, a false update, keygens, etc.
Have a look at this tutorial on making a system image & once the machine is cleaned (Do NOT make one now), make & keep a couple of these around. Next time something like this happens, it can save you a lot of time. Backup Complete Computer - Create an Image Backup