MichaelH

See what happens if you use a new query–change

query_posts( $args );
if (have_posts()) : while (have_posts()) : the_post();

to

$my_query = new WP_Query($args);
if ($my_query->have_posts()) : while ($my_query->have_posts()) : $my_query->the_post();

See The Loop for examples

Didn’t test but something like this would exclude pages with the ids of 2,5,12,14,20:

$args = array(
  'post_type' => array( 'page' ),
  'post_status' => array( 'publish' ),
  'orderby' => 'parent',
  'order' => 'asc',
  'posts_per_page' => 900,
  'post__not_in' => array( 2, 5, 12, 14, 20 )
);
query_posts( $args );

Not sure how or why you would have two sites using the same web-root folder — at least that’s what it seems.

Also make sure your WordPress and Site addresses are correct in Administration > Settings > General

Just because you decide to not display the custom field module does not disable any functionality regarding custom fields except that you don’t see the module in those screens.

Just use the automatic upgrade under your Dashboard -> Updates

Or if you want to do it manually, see Upgrading WordPress Extended.

To make WordPress available at http://mysite.com in Settings->General, change the Site address (URL) to http://mysite.com and put this index.php file in your web-root folder (it is the same folder that contains the staging folder)

<?php
/* Short and sweet */
define('WP_USE_THEMES', true);
require('./staging/wp-blog-header.php');
?>

There was this thread last year that might help you:
http://wordpress.org/support/topic/remove-youre-using-a-old-and-buggy-browser?replies=19