> The -* is what I typed in the scan rules 
> because I didn't want the whole site copied

You can't do that - you MUST capture html files, or httrack 
won't be able to detect the PDF links!

However, you can use filters such as:
-* +www.yoursite.com/*.html +*.pdf

(or +www.yoursite.com/*.asp is the site is asp-driven, 
etc..)