autocomplete on a multi value - custom field
If you modify your hook_form_alter to loop through the $delta of field_organization it should work for you on multiples...

/**
 * Implementation of hook_form_alter()
 */
function org_ac_form_alter(&amp;$form, $form_state, $form_id) {
  if ($form_id == 'user_profile_form') {
    foreach($form['field_organization'][LANGUAGE_NONE] as $delta =&gt; $field) {
      if(is_array($field) &amp;&amp; is_numeric($delta)) {
        $form['field_organization'][LANGUAGE_NONE][$delta]['value']['#autocomplete_path'] = 'org_ac/autocomplete';
      }
    }
  }
}