Error 101 after upgrading WordPress

We have just updated to WordPress 3.1.3 by following the WP manual install tutorial. Note: This is a Network-enabled (multi-site) install.

After uploading the new files, we now get the following error for ALL pages in the blog:

Error 101 (net::ERR_CONNECTION_RESET): Unknown error.

Any ideas? Here are the examples of our logs when the error occurs, and some of the WP-important files:

error_log

[Tue Jun 07 15:40:01 2011] [error] [client 10.10.0.3] PHP Warning: require(/var/www/html/root/wordpress/wp-includes/load.php) [function.require]: failed to open stream: No such file or directory in /var/www/html/root/wordpress/wp-settings.php on line 19

[Tue Jun 07 15:40:01 2011] [error] [client 10.10.0.3] PHP Fatal error: require() [function.require]: Failed opening required ‘/var/www/html/root/wordpress/wp-includes/load.php’ (include_path=’.:/usr/share/pear:/usr/share/php’) in /var/www/html/root/wordpress/wp-settings.php on line 19

[Tue Jun 07 15:40:01 2011] [error] [client 10.10.0.4] PHP Warning: require(/var/www/html/root/wordpress/wp-includes/load.php) [function.require]: failed to open stream: No such file or directory in /var/www/html/root/wordpress/wp-settings.php on line 19

[Tue Jun 07 15:40:01 2011] [error] [client 10.10.0.4] PHP Fatal error: require() [function.require]: Failed opening required ‘/var/www/html/root/wordpress/wp-includes/load.php’ (include_path=’.:/usr/share/pear:/usr/share/php’) in /var/www/html/root/wordpress/wp-settings.php on line 19

wp-config.php

define('WP_HOME','http://www.mysite.com');
define('WP_SITEURL','http://www.mysite.com');

define( 'MULTISITE', true );
define( 'SUBDOMAIN_INSTALL', false );
$base = '/';
define( 'PATH_CURRENT_SITE', '/' );
define( 'SITE_ID_CURRENT_SITE', 1 );
define( 'BLOG_ID_CURRENT_SITE', 1 );

.htaccces file (in wordpress root directory)

RewriteEngine On
RewriteBase /
RewriteRule ^index.php$ - [L]

# uploaded files
RewriteRule ^([_0-9a-zA-Z-]+/)?files/(.+) wp-includes/ms-files.php?file=$2 [L]

# add a trailing slash to /wp-admin
RewriteRule ^([_0-9a-zA-Z-]+/)?wp-admin$ $1wp-admin/ [R=301,L]

RewriteCond %{REQUEST_FILENAME} -f [OR]
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^ - [L]
RewriteRule  ^([_0-9a-zA-Z-]+/)?(wp-(content|admin|includes).*) $2 [L]
RewriteRule  ^([_0-9a-zA-Z-]+/)?(.*.php)$ $2 [L]
RewriteRule . index.php [L]