> 1 - Is there any way I can specify for a specific query 
to 
> generate a specific .htm filename.
> e.g index.php?> action=displaycat&catid=178&customheader=custom-header178
> produces:
> examplefilename.htm

Not really. Disable default MIME types if necessary, or 
define ones (such as php <-> text/html), but you can't do 
that on a specific URL.

> 2 - Is there any way of buidling in a directory 
structure? 
> So that you could specify certain php queries to download 
> to specific directories?
Same remark: only global build structure, possibly user-
defined, can be selected - but not yet for a specific link.

> 3 - In the generated mirror the filenames are as such :
> index8fff.html
> but the links to pages are as such:
> <a href="index8fff.html?> action=displaycat&catid=195&customheader=custom-
header195">
> I do not want the anchor texts to be generated with the 
> query string in the them (as search engines may avoid 
> this). I want the anchor to be:
> <a href="index8fff.html>

Set Options / Build / Hide query strings