Setting editor properties that wysiwyg_editor_settings_alter() can't touch.

I'd like to override a bunch of the CKEditor dataProcessor.writer rules, preferably in a transportable, without-patching-ckediter-3.0.js way. If I didn't care about doing things the Drupal way I would do something like:

CKEDITOR.editorConfig = function( config ) {
//... bunches of config
}

CKEDITOR.on( 'instanceReady', function( ev )
    {
        // Ends self closing tags the HTML4 way, like <br>.
        ev.editor.dataProcessor.writer.selfClosingEnd = '>';
    });

A good way to do this using the WYSIWYG API, I don't know. Looking through the code, it seems like wysiwyg_editor_settings_alter() adds keys and values inside CKEDITOR.editorConfig = function( config ) {}, but I need to add something after. Next thought was to try a custom plugin using hook_wysiwyg_plugin(), but I couldn't seem to get things working:

function mymodule_wysiwyg_plugin($editor, $version) {
  switch ($editor) {
    case 'ckeditor':
      return array(
        'cked_advanced_config' => array(
          'path' => drupal_get_path('module', 'mymodule'),
          'filename' => 'my-additional-config.js',
          'load' => TRUE,
          'internal' => FALSE,
        ),
      );
  }
}

Right now I have the .js kludged in there with drupal_add_js() that only fires if there's a CKEditor on the page, but I'm sure I'm missing something. Any pointers in the right direction?