The first thing I would suggest is to go to a clean PC and download a copy of Kaspersky Rescue Disk 10 (ISO), and either burn that ISO image to disc or else use something like Linux Live USB Creator to make a bootable USB drive from the ISO image file.
Once you have KAV prepped and bootable, boot your PC from the KAV disc. If it boots successfully, then you should be able to configure your network adapter, and start the KAV suite. Have it fetch it's updated definitions, then perform a full scan and clean of the entire system. This may be a lengthy process, and may take even longer if you haven't cleaned your system drive of temp files and other trash in a while. On a fairly clean system, I've seen KAV finish up in about 4 to 6 hours, but on a system that hasn't been cleaned since it was built... the process tended to take about 3 days (of course, this particular system had a very large hard drive and more than half of the drive's contents were trash).
I've successfully removed several root kits, and polymorphic malware variants using KAV, often with little or no damage to the system files. However, if KAV does clean it up, yet the system is still not booting correctly, then you might be best off using a Knoppix disc to load the system up so that you can evacuate any personal data you want to backup so that you can wipe the system drive and reload the OS. If you have to go this route, which should be a last resort, be sure to use 'gparted' from the knoppix disc to (a) reset the hard drive's meta-table, then (b) re-create your disc partitions, and (c) set the drive's flag to 'boot' so that it'll accept a bootloader. I personally never leave partitioning to the Windows installation disc, regardless of version, because I prefer to customize my partitioning schema. Also, I recommend creating a minimum of 2 Primary partitions, provided that the system only has a single hard drive. The 1st partition should be C: (system), and the 2nd partition should be D: (storage). After the partitions are created and the OS is installed, I tend to remap my personal folders to the D: drive.
Example: right click "My Documents", select properties, click the Location tab, and replace C:\Users\yourusername\... with D:\Users\yourusername\... (adjust this according to your personal naming conventions, username, etc).
The reason for moving your personal files into D:\Users\ is to segregate your personal data from system data. This is a good practice to make a habit of, because it makes it so much easier to blow away your system drive and rebuild without having to worry about loosing your personal files, such as documents, pictures, videos, etc. Another option is to remap the personal folders to an external storage system, such as a file-server, NAS, or SAN, but that option can be kinda dicey if you don't always have that external storage system up and online before all of your other systems are booted. Depending on the complexity of your environment, this may or may not be an option.
Anyways, best of luck... and if this helps someone else with a similar problem, all the better.
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