No matter whether your other HD is internal or external, if it was connected to this computer it could be carrying infected files, that goes for any flash drives, any CD/DVDs you burned. Any writable media that touched that machine after it was infected COULD be infected, that doesn't mean it is, it just means you need to remove everything, disable autorun of cd/dvds and flash drives and then scan them one by one once you have your primary HD (and CPU/memory which are cleared on shut down but generally reloaded by an evil startup service) clean.
I suggest you remove everything but your primary HD. Then try downloading one or more of the exes for
rkill and run them and reboot over & over until you are clear. Then run malwarebytes and run a complete virus scan. If you don't have any anti-virus software then download and run Microsoft Security Essentials and run a full scan. Then reboot again. Finally as I said above, disable autorun and then slowly insert HDs, flash drives, and CD/DVDs you made while at risk and do a full scan on each.
This
may work. Viruses can be really nasty.