New hard drive or reformat?

You could run diagnostics on the machine. Boot in safe mode and set up a chkdsk /f the slower but more thorough chkdsk /f /r (file, bad sector check). This will happen on the next boot. This may be worthwhile.

Given you have the vista CDs I think it's simpler and faster to simply backup the mess. Clean install and see how you go. Nothing lost except maybe some rubbish.

Ok update so I found a virus on the computer got rid of it and now it runs smoother. Boot time is still 20 min. I am not sure what to do about that any ideas? I want to try and not redo the windows their is alot of stuff to transfer back.