wp-includes errors in 3.5.1 upgrade

I’ve just downloaded the 3.5.1 zip file and followed the instructions (http://codex.wordpress.org/Updating_WordPress) for the manual upgrade (automatic upgrade wouldn’t work for me, even with php5). When I upload the wp-includes directory I get the following message from net2ftp:

Warning: ftp_mkdir() [function.ftp-mkdir]: 5745 Kbytes used (0%) – authorized: 1536000 Kb in /home/mainhost/public_html/file-manager/includes/filesystem.inc.php on line 986

For reference, I have replaced wp-admin and wp-includes directories and manually replaced the necessary files in wp-content. I have also renamed my current theme to include “-old” as per esmi’s instructions in various other posts addressing users with similar problems. Unfortunately, none of those resolutions seem to work for me. I have tried reuploading multiple times, but when I try to access the login for my site I get this message:

Fatal error: Call to a member function register_handler() on a non-object in /home/a2297728/public_html/wordpress/wp-includes/media.php on line 953

When I look to the media.php file lines 951-954 it reads:
function wp_embed_register_handler( $id, $regex, $callback, $priority = 10 ) {
global $wp_embed;
$wp_embed->register_handler( $id, $regex, $callback, $priority );
}

I’m fairly new to php so I really have no clue at all what is going wrong. My site is: http://www.charlottedupre.webatu.com/wordpress

I’d really appreciate any help provided, thanks!!