removed symbolic link to php.cgi, instead COPIED php.cgi file.
CGI does not resolve symbolic links. If the Action you define in .htaccess points to a symbolic link that resolves to php.cgi, CGI will try to execute the link.
However, directories can be linked. So instead of making a link from cgi-bin/php.cgi to ~/software/php/cgi-bin/php.cgi, make a link from cgi-bin to ~/software/php/cgi-in. The linking chain will work as long as the final destination is a directory containing the real file.