Hi Troy!
I'm not really sure what you are trying to do with the script, but you've got a couple of errors that I can see at a glance.
I think this bit:
# Print Header.
$output = qq|<div><table width="80%" border="3" cellspacing="0" cellpadding="2" bordercolor=#CCCCG><tr><td valign="top" width="50%"><font face="Arial" size=2><a class="link" href="$url"><font face="Arial" size=2 color=#FFFF00><b>$category_name</a> <small class="numlinks">($numlinks)</small>
\n|;
foreach $subcat (sort @subcat) {
($description) = @{$category{$subcat}}[2];
is stuffed up. Unless I'm missing something, you really shouldn't have the $category_name link in the header. I also can't see any closing </font> tags for the fonts you've specified.
I would suggest you get a fresh copy of the site_html_templates.pl file and try again, concentrating more on making sure your html is 100% and what you've done is logical.
If you're still stuck feel free to ICQ me on 174398215 to have a chat about it.
Good Luck!
Matt