This takes the youtube video ID stored in a custom field and adds a full Youtube URL to the content to allow the video plugin to easily index it.

gistfile1.php

<?php

/**
 * Takes the youtube video ID stored in a custom field and adds a full Youtube URL to the content to allow 
 * the video SEO plugin to index it.
 * 
 * The video URL is added to the top of content to make it override other video's in the post.
 * 
 * @param string $content the input content field.
 * @param array $vid the video array for the post.
 * 
 * @return string $content
 */
function fix_content_input( $content, $vid ) {
  $youtube_id = get_post_meta( $vid['post_id'], 'video', true );
  $content = "\n" . 'http://youtube.com/v/'. $youtube_id . "\n" . $content;
  
  return $content;
}
add_filter( 'wpseo_video_index_content', 'fix_content_input', 10, 2 );