+1 Hameister. Clean install is the way. To me it's best to install Windows with your wireless turned off and any network cables unplugged. It is safer to do a purely offline Win7 install in this manner. If you want to save time you can always use Windows Updates Downloader to download all the updates for your kernel (meaning x32 bit or x64 bit depending on what Windows you have) as files in advance, BEFORE installing Windows. You can save those update files on a USB stick and use them later on to update Windows offline after its installation is finished.
http://www.windowsupdatesdownloader.com/Default.aspx
Also get the latest drivers for all your devices in advance, BEFORE you start the Windows install. Best to have them saved on a USB stick in advance, alongside the updates. It will simplify the process and it also means that you'll be able to update everything on your fresh Windows installation without having to go online at all.
Once everything is updated make a full backup of your Windows disk BEFORE adding anything else. This way you'll be able to get your system back as it was at this point, if something goes wrong with any program installs. Once the backup has been created and verified, install security software. I recommend Comodo Firewall (free), Avast! Free antivirus, MalwareBytes' Antimalware and KeyScrambler (those last two are not free for the full featured versions, but they are worth buying). These programs work very well together, I have installed this setup on many computers so far without a hickup. Make sure you get them before you start the windows install, and copy them on your USB stick. This way you'll be able to install them completely offline, after your first backup.
Once all that is done go online for the first time, activate windows, get any updates that are left, and update your antivirus definitions. Install any other software you need, then make a second backup (incremental this time, so only what has been added after your previous backup will now be included to your backup files). After this is done make a copy of this backup to a differrent disk, verify both copies to make sure there's no corruption, then store the disk containing your second backup copy away from the computer. This will be your lifeline that will get your system back from the dead in case the disk that holds your initial backup develops bad sectors or dies.
It would also be a good idea to familiarize yourself with light virtualization and snapshot solutions if you haven't done so already. For more info on this have a look at my guide here:
http://thessdreview.com/Forums/software/2247.htm