*URGENT* Reinstall Windows while keeping program settings

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I need to reinstall Windows 7 on a friend's machine, as it had been hit by a nasty malware infection, and the effects of the infection are still lingering even after they have been removed. I would just back up the files, reinstall the OS, and call it a day, but this person isn't very technically literate, and they have several programs installed, namely Microsoft Office and iTunes. I want to be able to wipe the drive and reinstall the OS, while keeping everything else as it was. Is this even possible?

If reinstalling the OS isn't an option, there is this one particular issue I need to fix with Internet Explorer. With "protected mode" enabled, this person is unable to access certain bookmarks. Bookmarks that don't use https work fine, but ones that do, like Google, Facebook, and his online banking, refuse to open. On anyone else's computer, these would work just fine with protected mode enabled. No, telling this person to use another browser isn't an option. I hate Internet Explorer and it amazes me that people still use it, but I'm dealing with someone who really, really doesn't know much about computers, and just wants his machine to work how he expects it to.

firefox works is close enough to IE in workings, you might want to try that.
also, there might just be a setting in IE under protected mode; seeing that it's only https sites that don't work, i assume it's an issue with tracking cookies, secured sites need some cookies to be set to secure the connection, and he strongest protected mode in IE prevents that from happening (no, i don't really know where that setting is, but i seem to remember that it indeed exists; a toggle between "allow but instawipe" and "don't allow altogether").

if that doesn't work, first try to reinstall IE clean; just download a new browser first, kill IE trough the "windows components" part of the program manager, and reinstall there. (make sure to export the bookmarks and stored passwords to a file first, as this process will kill those).

secondly: windows' installer allows an option to "repair" which only reinstalls windows and the primary software, leaving the rest of the disk alone

finally; installing iTunes and office isn't that big of a deal, if those are the only things, both got an easy download on their respective websites, assuming you got an activation key (for the office part), but i assume you do., if the first two options didn't work, just reinstalling these programs is an easy fix.

i myself clean install windows every so often, and then reinstall such software manually as well; this has the added bonus of making sure that the latest versions are up, and cleaning up compound junk from a year of updates

As far I am aware http://windows.microsoft.com/en-us/wind ... your-files can do exactly what you are asking for.

About IE - install Firefox or Google Chrome, import bookmarks from IE and call it a day. Tell your friend it isn't save to use IE anymore and show him the newly installed browser. It won't take long for him to get used to it.

I know little about Windows, but as far as I know most programs keep their settings in the registry, not in files in the user's directory. Does this tool back up those settings too?

On the other hand, depending on the specific malware, it might not be safe to restore everything either. The program may infect program files, documents or settings which can retain the infection after a reinstall.

I managed to get protected mode working under IE, by uninstalling and reinstalling the updates for it. The owner wanted his machine back so I let him take it home, but it was running quite slowly before I gave it back to him, and AVG was experiencing some issues I think I'm going to ask his wife what programs she uses, so that I can just reinstall the OS and only install the programs they actually use. Backing up documents and pictures is trivial, it's transferring a Microsoft Office license and an iTunes authorization that really stump me. I know they use both of those programs, but I'm not sure what else is on there that they actually use.

I just want to get this over and done with. I feel bad for not finishing work on his machine.

Did you try a scan in safe mode with Malwarebytes free edition? It usually works to remove malware and avoid reinstallation of operating system. It's not an antivirus but a complementary software.

Also, you can scan for rootkits with tdsskiller.exe, a free downloadable utility from Kaspersky. You don't need to remove the current antivirus to use tdsskiller. Tdsskiller will scan for rootkits in less than 1 minute.