I think if someone could point me in the right direction I could figure this out

1- which file do I edit affect what links show up in the topbar

2- which file to edit what shows up in what I think is called the header. (the bar just below the logo.)

views/default/navigation/topbar_tools.php

you'll need to tweak the code inside the loop that spits out the menu items

      <?php
            foreach($alphamenu as $item) {
                echo "<li><a href=\"{$item->value}\">" . $item->name . "</a></li>";
            }
     ?>

I think this is to be done to my theme right? nevermind it's not in there.  this is a change to a core file right?

nope right where i said above

i checked yr theme to make sure no conflict ;-)

u r safe