There are no problems with running a personal script after downloading of the dedicated Special:Notifications page, but I do not know how to do it after downloading of the notifications popup as
<div style="display: block;" class="mw-echo-overlay"> </div>
It seems to me that hooks added with
jQuery(document).ready(
…)
are not called then. There are docs at http://api.jquery.com/ but I am not a DHTML expert and can’t find easily the thing I need. Suggestions?