You didnt mention the size of the drives...

With the price of externals today I cant imagine your saving any money by doing what you are doing especially since you have to ask in a forum about existing viruses you say you have already and assuming they do have a virus and just not defective in general . You can buy thumbdrives bigger than an old hard drive or get cloud. If you think a cloud is made out of water vapor then I would suggest using a PS3 for your computing needs.