Virus help needed:  Parallels:  Windows XP virtual machine

I will preface my remarks by apologizing in advance for my lack of technical sophistication, inexperience with Windows, and experimental approach to providing tech support to myself. It just happens to be the case that I have infrequently needed to use computers in my work life, aside from operating cash registers equipped with POS systems; and have used Macs at home for my entire life as a computer user. (I only started using the internet about nine years ago, although I am 44 years old.)
Here is the background of my situation:
In Winter 2008, in anticipation of training for and entering into a new line of work, I purchased a MacBook3,1. Because the new line of work would regularly require me to use Windows-based applications, I purchased Parallels 3.0 at the same time that I purchased the MacBook.
I installed Parallels 3.0 from a disk, installed Windows XP, and set up a virtual machine. I used this VM for more than a year and a half without incident. A one-year certificate for Kapersky Internet Security was included with the purchase of Parallels. In the meantime, I upgraded to Parallels 4.0 in Winter 2009. The upgrade was accomplished via download, using the product key that I'd purchased.
At some point, my Kapersky certificate expired. I was unclear (though I am no longer) as to whether running Windows on Mac was any different - - i.e. more secure -- than running it on Mac. I made a mental note to look into the whole matter and avoided using the internet while working in the Windows VM.
At some point, however, I lapsed in my practice of avoiding using the internet while working in the Windows VM. I ended up with a virus, of course.
That said, I had (and have) a back-up of what I believe to be a pre-virus Windows VM. I used this back-up to add/create a new VM. I was prompted to back up the back-up before so doing; and was also prompted to update the new machine to Parallels 4.0. Which I did. The update to Parallels 4.0 took a long time.
In the interim, I had moved some working files from the infected VM (which themselves were infected, judging from all indications) into the Mac OS for temporary storage.
My memory of what I did and what happened next is imperfect. But here it is in gist and to the best of my recollection:
When I booted the new machine, I received a message to the effect that I should install Kapersky Internet Security -- although the certificate I'd purchased along with Parallels 3.0 had ostensibly expired. I installed Kapersky. Then I received a message that I needed to update Kapersky. Which I did. This, too, took a long time.
I then cloned the new machine.
I then rebooted the new machine and moved the infected files into it. I scanned the infected files for viruses and nothing showed. Then I opened one or more of them to see if things were operating satisfactorily. The virus, I soon discovered, was present in the new machine. At some point I also received a message to the effect that the Kapersky software itself had been altered? And subsequently received a message prompting me to accept or not accept a rule relevant to internet security/Kapersky. (I forget exactly what I did in response.)
I then booted the clone -- into which I had NOT moved the infected files. The virus eventually showed up there as well. I also received a message to the effect that Kapersky may not be up to date -- even though the VM was a clone of a machine that was ostensibly recently updated. AND I received the same massage prompting me to accept or not accept a rule relevant to internet security/Kapersky. Which I ignored.
I have since deleted the new machine and its clone. I have backed up onto CD my infected work files in case I may learn in the future of some way of disinfecting them.
What do I do from here? I am interning in my new line of work, and need to get Windows up and running ASAP for that reason. I still have the back-up of what I believe to be a pre-virus Windows XP VM.
Sorry to be so broad and so vague.
Thanks for any feedback.
--Kim

Kaspersky has a tip area of what to do. So does Norton Community. And one of the best anti-malware is actually free, Microsoft Security Essentials.
A lot of poeple use MalwareBytes and SuperAntiSpywear in a crunch or regularly.
http://blogs.zdnet.com/security/?p=4818
http://www.superantispyware.com/
http://www.malwarebytes.org/
http://www.microsoft.com/security_essentials/support.aspx
What to do:
http://www.microsoft.com/security/portal/Shared/Help.aspx
http://www.symantec.com/norton/support/premiumservices/premiumvirus.jsp
Vista and Windows 7 are more secure, there are still vulnerabilities in most browsers, plug-ins, and I'd say Internet Explorer 8 can be the most secure and reliable web browser on Windows.

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