You could try an Inplace Install provided that you don't have any files Encrypted. If you haven't used the EFS Encryption you can follow the directions here for an Inplace install
http://tinyurl.com/g4bv8
If you have encrypted the files you'll need to remove the HDD fit it to a USB Caddy and then recover the Encryption Key/s by following the directions here
http://tinyurl.com/orpmf
You may have to follow a couple of links from here as currently the MS Site is down for maintains or whatever. While you could use the drive as a Slave I find it faster & easier to just dump it into a USB Caddy and use that to save your Data & Encryption Key/S from as there is no messing about with jumpers.
When you do an Inplace install you'll keep all your Software settings and so on but if you have a Registry error you'll get to keep that as well so to make sure that you don't have a hardware problem drop in a Live Linux and Boot off the Linux CD if that works without a problem you can then attack Windows knowing that the problem is there and you don't have a hardware issue that needs looking at. The Live Linux will run entirely from RAM and will have no affect on your current HDD/s with Windows on them.
Col