Wordpress - WordPress 3.9 - Trouble Editing TinyMCE 4.0

The strings was new, not more for your requirements.

This is the new content of the hook.

array (
  'selector' => '#content',
  'resize' => 'vertical',
  'menubar' => false,
  'wpautop' => true,
  'indent' => false,
  'toolbar1' => 'template,|,bold,italic,strikethrough,bullist,numlist,blockquote,hr,alignleft,aligncenter,alignright,link,unlink,wp_more,spellchecker,wp_fullscreen,wp_adv',
  'toolbar2' => 'formatselect,underline,alignjustify,forecolor,pastetext,removeformat,charmap,outdent,indent,undo,redo,wp_help',
  'toolbar3' => '',
  'toolbar4' => '',
  'tabfocus_elements' => 'insert-media-button,save-post',
  'body_class' => 'content post-type-post post-status-draft post-format-standard',
)

Also change the strings inside the array in your source to:

function myformatTinyMCE( $in ) {

    $in['toolbar1'] = 'bold';
    $in['toolbar2'] = 'formatselect';

    return $in; 
}
add_filter( 'tiny_mce_before_init', 'myformatTinyMCE' );

But see also this test plugin Gist 9758082 and this thread for WP 3.9 and the new TinyMCE 4.0 to understand the topic.

Forcing Toolbar2

To show always the toolbar 2, without use the button wp_adv add the follow source to a plugin.

add_action( 'plugins_loaded', 'fb_force_show_toolbar2' );
function fb_force_show_toolbar2() {
    set_user_setting( 'hidetb', 1 );
}

BUT, now the hint for the value wordpress_adv_hidden. In the next WordPress version, after 3.9 will restore the old hook wordpress_adv_hidden to toggle the toolbar, see ticket 27963. Then is possible to to use the follow source. $in['wordpress_adv_hidden'] = FALSE;

add_filter( 'tiny_mce_before_init', 'myformatTinyMCE' );
function myformatTinyMCE( $in ) {

    $in['wordpress_adv_hidden'] = FALSE;

    return $in; 
}

One change is that:

theme_advanced_buttons1 is going to be changed to:

toolbar1 which allows you to update the buttons so my new function will look something like:

function myformatTinyMCE( $in ) {
    $in['toolbar1'] = 'bold';
    $in['toolbar2'] = 'formatselect';
    return $in; 
}
add_filter( 'tiny_mce_before_init', 'myformatTinyMCE' );

Also it looks like formatselect is not really favored as much in this iteration. Should probably be converting over to styleselect as it allows more options and customizations (such as nested styles) and also goes with a more minimalist design.

Another gotcha is alignment options have been changed from justify to align like so: alignleft, aligncenter, alignright, alignjustify.