If you go to anyone other than Microsoft, such as Magic Jellybean or anyone else, for things you could easily get directly from Microsoft, then you run the risk, as you have already found out, of downloading a virus that could make the problem all the more worse.
If you go the Microsoft webpage, located at http://www.microsoft.com/genuine/downloads/FAQ.aspx?displaylang=en, you will find all you need to know about their Genuine Advantage System, including the answer to your particular question. If you scroll about two-thirds down the page, you will find a section entitled, ?After I receive the kit, how do I convert my software to genuine Windows?? Read all the questions in this section first, because it will tell you why you need to do the system scan that they are going to ask you to do before you can download the Product Key Updating Tool. This section is actually for people who have either bought or obtained "an electronic license", but if you DO have a new CD and if it IS a valid Microsoft Windows CD (and never used before) then it should work if you type in the product key code from that. (For information on how to know if your software is genuine, go to the webpage at: http://www.microsoft.com/resources/howtotell/en/default.mspx).
In the first question of the section I mentioned above, it says:
Q: I purchased an electronic license and received the product key in email; what do I do?
A: To convert your counterfeit Windows XP software to a genuine copy of Windows XP using the new product key, you will need to download and run the Windows Product Key Update Tool on the same computer you used to purchase the electronic license for Windows XP. Visit http://go.microsoft.com/fwlink/?LinkId=45668 to download the Windows Product Key Update Tool. The Windows Product Key Update tool will guide you through the conversion process and convert your counterfeit Windows XP to a genuine copy of Windows XP.
This will lead you to another webpage, which will instruct you to do the scan before you download the product key updating tool. It also has the link for the tool itself. This should answer your question.
There is a chance that the scan would not be able to fix your copy of Windows, if it had been tampered with by the people who sold that pirated copy. If so, then you would have to re-install Windows. For that, I would recommend an upgrade version. That would not require that you re-install everything from scratch. You may, however, run into problems when you try to install the upgrade and it tells you that you cannot ?upgrade? because you have already done so and have all the updates already on your computer. There is a fix for this to. You would have to uninstall all of the updates and search the Microsoft Knowledge Base, at support.microsoft.com or this c/net website to find answers for that.
If what you have is a FULL version, you are not supposed to be able to do it, but I have tried and it worked for me. I would recommend having a good backup before you try this, though. With Windows running (don?t try this from a bootup or it will NOT work), put in your Windows CD and install it from there. It MAY work like an upgrade CD, but if it doesn?t, then just use your backup program to run a recovery to get it back to where it was before you tried it.
Good luck, and I hope this works for you!