A thorough search of the server turns up just two files named precisely httpd.conf. Their paths are
/private/etc/apache2
/private/etc/apache2/original

Both have the desired path in them /Library/WebServer/CGI-Executables

There are variations on the name, all with suffixes such as .pre-update and original. Even they have the desired path though.

I did find a hidden file name .httpd.conf.swp with no apparent reference in it though much of it appears to be binary.

So I remain at a loss as to where Apache is getting the path it's using.

The URL is http://domain.com/cgi-bin/my.cgi

And that works IF I locate the scripts to: /Library/Server/Web/Data/CGI-Executables
 
On Feb 1, 2015, at 12:28 PM, Eric Covener <covener@gmail.com> wrote:

On Sun, Feb 1, 2015 at 12:06 PM, James Cook <james.jim.cook@gmail.com> wrote:
What would cause Apache to ignore the httpd.conf assigned path and how can I correct it?

Most times it's the user looking at the wrong configuration file
(completely wrong httpd.conf, overridden Include, looking at unused
virtual host).  What URL do you request and what htaccess files might
exist along the way?