After the upgrade process is complete, you will be presented with a link to your Admin Control Panel. Before clicking this link, you should open up your FTP client application again and browse to the /core folder inside your forums directory.
You should delete the entire core/install directory. Doing so will not impact vBulletin's operation on your site. Once you have deleted this directory, you can return to the installer script and click the link to enter the Administrator Control Panel of your freshly installed vBulletin!