Atahualpa 404 redux

I seem to have the problem described in ( Jacob Gotwals post of a year ago . The instructions for making a 404 page for Atahualpa that I find there seem to be out of date, as I do not find the phrase “<?php get_header(); ?>” in my copy of index.php. Is there another solution to Jacob’s problem (now mine) or uptodate instructions for making a 404 page?
Go to http://www.junctionra.ca/jra-archives/, and click on Minutes for Nov. 10, 2011 to see the problem. The link to page http://www.junctionra.ca/wp-content/uploads/2010/11/JRA-Minutes_10-Nov-2011.pdf, a file which doesn’t exist, displays what looks like a search results page!