I like the answer of d79 for the first part.
For the queries, I think it would be better to extend WP_Query class ( i.e. WP_Query_Custom ) and have one copy for each domain. Then you can load the file you need based on the domain in the functions.php file, and so you don't need to change in the future your calls everywhere you use WP_Query_Custom, even if you need to add more domains and different versions of WP_Query_Custom.
//in functions.php
$mydomain = str_replace('.', '_', $_SERVER['SERVER_NAME']);
require_once("path/to/my/classes/$mydomain/WP_Query_Custom.php");
//In each path/to/my/classes/$mydomain/WP_Query_Custom.php
class WP_Query_Custom extends WP_Query {
function __construct( $args = array() ) {
// Force these args
$args = array_merge( $args, array(
'post_type' => 'my_custom_post_type',
'posts_per_page' => -1, // Turn off paging
'no_found_rows' => true // Optimize query for no paging
) );
add_filter( 'posts_where', array( $this, 'posts_where' ) );
parent::__construct( $args );
// Make sure these filters don't affect any other queries
remove_filter( 'posts_where', array( $this, 'posts_where' ) );
}
function posts_where( $sql ) {
global $wpdb;
return $sql . " AND $wpdb->term_taxonomy.taxonomy = 'my_taxonomy'";
}
}
The example class is copied from extending WP_Query