Well, here's a thread where we talked about adding something to the notifications menu:
www.vbulletin.org/forum/showthread.php?t=286095 . It's basically the same thing that 's done in the plugin you posted (but of course yours is more complicated because it actually checks something instead of using a constant). If you can figure out the code to get the number of notifications you want, you should be able to follow that example to display them in the menu.