Reinstalling Windows 8 in Optibay Drive.

Hey,

I've got my 2010 MBP set up with an SSD in the main bay and a traditional HD as my secondary in place of the sueprdrive. While setting that up, I originally installed windows 7 using a dvd on the traditional HD prior to installing the SSD and removing the internal superdrive. I then wiped the OSX partition on the HD, put the SSD in the main bay, placed the HD in place of the superdrive, and installed OSX on the SSD. A couple of months later, I upgraded the windows 7 to windows 8.

Now the problem is that I installed a screenshot program to complete a project approaching its deadline on windows 8. The things is that it came with a virus, one of those autorunning scam programs that says you have 456 viruses on your PC so give me your credit card number to remove those viruses.

Now, I want to do a clean install of windows 8 on that partiton. I know there may be ways of removing the malicious program but I won't have any piece of mind using the windows partition knowing that it was infected. Also on a side note, is my data on my OSX partiton in danger because of that program on windows 8?

Any suggestions on how to reinstall windows 8 (or 7, then upgrading to 8) without putting the HD and superdrive back in their places?

Thanks in advance!