MBR is altered due to virus-needs fixed

Ok so here is my problem from what I can gather. My PC was infected with malware and viruses causing all kinds of major issues. I was helped in the Malware Removal forum and it appears it is clean now. I have run and rerun all the software I was told to run and no new threats are turning up.

The problem is the MBR is coming up as "altered or infected". Now I try to run the Vista Recovery Console to do a boot recovery and mbr fix but it does not recognize the OS in the console. It is not even recognizing drives if I attempt to do a clean installation. The virus seems to have corrupted MBR making traditional fixes with the WRC not possible as is now.(catch 22?)

Also I cannot do any updates for Vista, the window just hangs when I try and use Windows update to check for updates. Having problems with installing USB devices too. I do have an Acer with a hidden partition to run the E Recovery but I want to just do a clean vista installation at this point and rebuild as I have everything I need on discs.

I'm not a pro at all this hence why I have come here for help and advice. How do I go about fixing the MBR and/or doing a clean vista installation?

 

:cry Thank you for your time kestrel13 this PC is really aggravating me. I really am at a loss if you can figure out this problem you are a gent and a scholar.