When creating an article choose "No Show Article", then set up the "article link" block, say on the "side block left" using "weighting" to have this menu show first, you can call this block anything you wish. The "No show Article" allows the article links block to include the article.
There also is a recent content wfsections block you can use in a similar way
The title of the article i.e. "Faculty" will automatically appear. This is a direct link to the article. Also, if you choose "No show info", when creating or editing the article, it will just be a plain HTML page without any other info.
I have a little example on a site I am building
HereOr, create custom links in a custom block, the paths to your articles of course appear in the browser address bar.
The php part I can't help with, no a coder, but if you do a search there is hacks or modules which allow you to add or include php scripts somewhere
You can hide the wfsections link in the Main Menu by going to modules in system admin, and go to the "order" column for wfsections, and change the order to "0". You can also rename the modules here, and the new names appear in the main menu. Any block can also be renamed in blocks admin
To take out the logo in the main index page you can go to the index page manager and choose "blank" but this leaves a space where the image would be, so
Go to yousite.com/modules/wfsections/index.php
and look for
echo "<table border='0' cellspacing='1' cellpadding ='3' align = center width = 100%>";
echo "<tr><td align = center><h4>".indexmainheader()."</h4></td></tr>";
echo "<tr><td align = center><h3>".sprintf($wfsConfig['indexheading'])."</h3></td></tr>";
echo "<tr><td align = center><h4>". _WFS_MAININDEX ."</h4></td></tr>";
taking out three of these lines removes all the logos and index info, but try them one at a time to see what it does i.e.
echo "<tr><td align = center><h4>".indexmainheader()."</h4></td></tr>";
this one removes the logo space, and so on