Okay, with layout.tpl.html unmodified and the modified code running at line 388 of ajasSearch.class.inc.php the first URL posted in this thread no longer displays an iframe on the results page. It does however return an iframe with the code below (the second URL posted in this thread):
http://www.domain.com/search-results.htm?AS_offset=10&AS_search=Search+here...>"></title></iframe></script></form></td></tr><br><iFraMe+src%3Dhttp://www.HackerSafe.com+width%3D900+height%3D1100></IfRamE>&advsearch=http://www.scanalert.com/help/scanner/5/rfi%3F
Now, when I run XSS Me against this page the ajaxSearch_form::sub shows green results (The character was not found unencoded in the result page), which is an improvement in my results. Although I get red results (The character was found unencoded in the result page) against ajaxSearch_form::search for semicolon, forward slash, quotations, and equals sign (; / " =).