The most complete answer to my newbie question seems to be this one, which unfortunately tells me, that I need to boot into my Windows 7 system ("must be logged into Windows 7 in a administrator account to be able to do a repair install"). Unfortunately this is not possible in my case.
http://www.sevenforums.com/tutorials/3413-repair-install.html
Cited from the source.
Do a Repair installation if:
A System Restore did not help fix your Windows 7. There is no other easier option left that can fix your Windows 7. You DO NOT want to do a Clean reinstall of Windows 7. You DO want to preserve your user accounts, data, programs, and system drivers. ITEMS THAT WILL BE RESET TO DEFAULT OR AFFECTED:
Sounds Services Visual Effects Settings Device Drivers - Be sure to have these handy to reinstall. They do not always remain after the repair (upgrade) install. You may lose the ability to sign on to MSN Messenger, to solve this problem have a look at this thread Unable to sign in to WLM. You may lose your custom themes due to not having permisions set on the old themes. Go to the hidden themes folder at C:/Users/(User-Name)/AppData/Local/Microsoft/Windows/Themes, then Take Ownership of the themes folder and you will now have all your themes back. It has been reported that you may also lose your Media Center gadget after doing the repair install. Windows Updates will need to be checked and reinstalled again. Warnings
You can only do a repair install with the same edition Windows 7 installation disc for the same edition of Windows 7 that you have installed. You cannot use a OEM Windows 7 "Factory" Restore/Recovery type of installation disc that came with or created from a store bought computer to do a repair install with. These can only be used do a clean install instead. You can do a repair install on a factory OEM installation with the latest official Windows 7 with SP1 ISO file here: Microsoft: Windows 7 Direct Download Links, and use Windows 7 USB-DVD Download Tool to create a bootable DVD or USB flash drive with the ISO to do the repair install from within Windows 7. You can use a retail OEM Windows 7 installation disc to do a repair install with. You can use a retail (full or upgrade) Windows 7 installation disc to do a repair install with. You cannot do a repair install with a System Repair Disc. A System Repair Disc is not a installation disc, and will only boot to the System Recovery Options screen. If you have a 32-bit (x86) Windows 7 currently installed, then you must use a 32-bit Windows 7 installation disc to be able to do a repair install with. If you have a 64-bit (x64) Windows 7 currently installed, then you must use a 64-bit Windows 7 installation disc to be able to do a repair install with. You can use a retail Windows 7 SP1 installation disc (ex: Technet (available), MSDN (available), or retail (when available)) to do a repair install with on a currently installed Windows 7 SP1. You can use a Windows 7 SP1 installation disc (ex: Technet (available), MSDN (available), or retail (when available)) to do a repair install with on a currently installed slipstream Windows 7 SP1. You cannot use a slipstream Windows 7 installation disc to do a repair install with on a currently installed Windows 7 SP1. You cannot use a slipstream Windows 7 installation disc to do a repair install with on a currently installed slipstream Windows 7 SP1. You can only do a repair install from within Windows 7. You cannot do a repair install at boot or in Safe Mode. You must be logged into Windows 7 in a administrator account to be able to do a repair install. You must have at least 8.87 GB + what is currently being used of free space (more if you have a larger installation) on the hard drive/partition Windows 7 is installed on to do a repair install. If you changed the default location of a user account's profile folder, then you will need to change it back to the default C:\Users location first. If you moved the default location of a user folder, then you will need to change it back to the default C:\Users\(user-name) location first. Update
Finally I did, what was recommended in this answer + recovered my files from the Windows.old directory. I had to install all the software again. But I could at least recover the configurations from the %APPDATA% folder.