As far as booting; that is the drive that system runs off of, loads os(operating system). Then, it can see and manipulate other drives attached(cd, external hd, floppies, thumb drives etc.); but is not 'booted' to them, is not just blindly trusting that drive and running it's software etc. (unless autoruns is on). So, if main drive is suspect, boot to a cd, or to another drive-with autoruns turned off; so the suspect drive won't run anything in it's boot when you go to it. Then, get data off, scan for malware etc.
http://ubcd4win.com/. If sys won't boot to another os, hardware then is much more suspect, and trouble shooting takes a right turn into that direction. Usually this entails, stripping devices (cd, floppy, hd etc.)out 1 by 1; seeking something not working right, halting rest of sys.
Malwarebytes is very good for removal and has been suggested; they have a forum too to help. Also One of the last sections of MB forum shows 1 by 1 all the different things malwarebytes handles very well. The instructions for handling each are step by step, but all the same; plus sometimes other info on virus too. There are vids on all this on google and utube for booting to linux, bart pe etc. from cd and handling all of this.
http://www.youtube.com/results?search_query=malware&search_type=.
http://www.bleepingcomputer.com/ is very good forum too.
As far as thumb drives go; it is best to tell computer you are removing one by right clicking safely remove drive icon near clock. This will make sure nothing is (especially) writing to that drive/device. Because if it is writing when you remove thumb, you can screw up that thumb drive, because it won't be able to write to the fat table/ table of contents the disk locations were files are. Thumbs usually come formatted with fat16; because it isn't patented. Can google a hp formatting tool to help.
Also, i wouldn't recommend anyone using a thumb to extend memory like vista allows. Because, these flash devices in thumbs aren't the best/best; and will fail after so many writes- of which memory storage gets a lot; so pushes these devices to earlier failure.
2 computers can be connected through a router, through usb or a cross-over cable, if not ad hoc through wireless cards; many videos around on these 'basics'.
Many, many times i've seen were a cd drive seems bad- but isn't. Besides cables, and making sure is on in bios; it can be some added microsoft filters (kinda like secondary drivers) that need edited out of the registry. Real ms advocates refer to these things not as error, mistake; but rather politely as an "undocumented feature"
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http://support.microsoft.com/kb/929461 after creating restore point.