Good morning mrsbeautiful05. I'd like to +1 Anshad Edavana's suggestion to do a clean install, esp. in light of your recent infection.
Upgrading can lead to a number of issues where as a clean install is just that - clean. You won't have to worry about any registry issues and/or any traces of your recent infection.
Back up all the important data / files you need somewhere else and then drop that CD/DVD in and let her run.
I believe one of the first windows (no pun intended ) that you will see will be the option to Upgrade or Install (it might say Custom Install) and then from there it's all pretty straight forward, enter Activation Key, agree to the EULA, etc.
As for the couple of other issues that no one seems to have addressed: the classic shell - shouldn't be an issue. Personally, I'm holding onto Win7 as long as I can but if you find the layout in Win 8 confusing / awkward, rest assured you won't be alone and it is being addressed, as per this post here by Budapest.
And if you find you'd like the Start Menu, ReviverSoft made this post, which seems like a good idea.
As for updating any and all apps, I would strongly suggest that you do all of that after you perform the clean install.
Not sure if you're using it or not but Secunia 2.0 (not 3.0) is very helpful and a great app when making sure your machine is patched and up-to-date. If you need a link to find it, please let me know.
Hope that's enough information for you and if you need anything else that I can help you with please let me know.