> Can I actually copy an entire website, which I was
> given permission to by the way, and customize it to
> become my own?> for me? And will it capture every single link or

Httrack does not make a copy, it create a static mirror.  If the site has
dynamic content, databases, forms, complicated javascript, or swf, those will
not be copied. Those are server side code, (code executed on the server.) 

The output from a server is html and related files. Those httrack will
capture.

The default is to convert internal links to relative file names. This allows
you to click on a mirrored page and go to the next page without a webserver
running on your machine.

For your case you don't want the footer (options -> Browser -> footer=null)
and don't want the conversion (options -> experts -> rewrite links=keep)