The scenario:

A PDF file is opened in a separate browser window.

The problem: How to create a link (image or text) in the PDF file
using either javascript or html to close the window to return to the
parent page.

In the PDF file, I tried using the javascript link action with 
javascript:window.close();

and

go to web page action http://www.website.dom target="_top"

Neither works.

I am certain this must have been done lots of times but I have been
unable to find a solution.

Try opening the PDF files in a  new "framed" window, in the top frame
put your javascript commands in a button.  In the bottom frame have
your PDF load.

Create an link to your framed page like this:

<a href="pdf_in_frames.html?file=myfile.pdf">Click Here</a>

Now in the recieving frames page (in the bottom frame) put some
javascript that gets the query string and loads the PDF.  See below.

<script>
window.location.href=window.location.search.substring(window.location.search.indexOf('=')+1);
</script>

Try it, it works.