First you need to format your computer, set up a fresh windows and get everything setup WITHOUT EVER connecting your Flash/iPod/Externals
Then you need to download a good antivirus (I would recommend McAfee or NOD32) and have it updated through the internet to match the latest virus signatures also WITHOUT EVER connecting your Flash/iPod/Externals
After you have done that, download iTunes from www.apple.com and connect your iPod and have it RESTORED (not updated) which should clean it out of any viruses or worms but will cause you to loose all your data stored on it
Next step will be to connect your external storage devices (Flash, E-HDD etc) and scan them for viruses using the software you have setup. If you had it updated, then it should clean your externals of all malicious softwares easily
Good luck, i hope this helps