TaZz,
It sounds like it did a
Custom install instead of a Upgrade install. See the screenshots in this tutorial (
Clean Install From Upgrade Vista) to see if they look like what you have seen instead. That would explain why all of your settings and programs were lost. This is almost like doing a clean install, except you have a backup of the old installation in C:\Windows.old.
I would try running everything from within the
C:\Windows.old\Users\(old_user) location to see if will still work. If it does, then you can simply copy everything in only that folder back into the
C:\Users\(user name) location to have it back. If it doesn't then you will need to reinstall the programs. My guess is that it probably will not work since there are just to many unknown locations that programs place files at that they need.