After having wrestled with a regular expression for almost 2 weeks I was able to complete the code needed to search and replace HREFs in <a> tags with some javascript. The code is as follows:

s/<a (.*?)HREF\s*=\s*"(?!(javascript|mailto|[#]))(.*?((FL(?{$w=250})|OV(?{$w=800})|TK(?{$w=350}))(\w|_)*?\.htm).*?)"(.*?)>
/<a href="http://www.orwd.com/blog/wp-admin/post.php#" mce_href="http://www.orwd.com/blog/wp-admin/post.php#" onClick="
w=window\.screen\.width-$w-12;
window\.open('$3','helpWin$i','top=0,left='+w+',width=$w,
height=650,top=no,status=no,toolbar=no,menubar=no,
location=no,scrollbars=yes,resizable=yes');">/gis;

I can happily blame Lynn Killam and my partner Fred Kush for this undertaking. I am very happy to tell you that it works beautifully.