I am aiming to take an exact replicate of a site so that I am able to
effectively link to the specific page once the page has been downloaded. At
present most links are broken when I use them in my application.

Unless I am mistaken previously if we had www.abc.com/index.php then this
would be converted to www.abc.com/index.html when HTTrack had downloaded the
file. 

Similarly www.abc.com/products/ is being converted to
www.abc.com/products/index.html.

All of the above are causing problems for me and I wondered if there was a way
in which the actual link could be preserved, by that .aspx, .shtml, .php, .htm
etc

I have looked at setting my own format of %h%p/%n.%t and this doesn't work
properly.

I have read this post where you were implementing the -%t option however I
have downloaded the latest version and this doesn't appear to be working. Has
this function been implemented as yet?
Any help appreciated.