> I found the problem. IIS interprets a path with a '.com' 
> in it as an executable, so they get blocked.

Argh! What a louzy server :(

> modify the domain information. For example: 
www.mysite.com 
> becomes www.mystie.c8m.
> Is there a way to do this in WinHTTrack?
Using the library, yes - but not using WinHTTrack.

You may use the same structure, but without "www.site.com" 
as suggested by one of the "build options" in winhttrack.

You could also use Apache server.