> of stuff.  It may be impossible with this program
> because the site is mostly flash based with many
> links in .swf files...

Exactly the problem. HTT finds links and downloads those.
It will download the swf but it is the swf that tries to download the content.
In the mirror it tries to download from the server on your machine. Since
neither a server or the files exist, it doesn't work.

The best you can do is extended parsing (attempt to detect all links) It'll
work if content location is passed as a parameter to the swf