I don't have any experience with HTML::FormatText, but LWP and HTML::TreeBuilder are rather dear to my heart. Try out the following code, I think it will get you closer to what you want. I just put the links in line with the text they were associated to, but you could easily print a footnote an push them into an array.

use strict;
use LWP::UserAgent;
use HTML::TreeBuilder;

my $ua = LWP::UserAgent->new;
my $page = $ua->LWP::UserAgent::get("http://www.databasefootball.com/b
+oxscores/scheduleyear.htm?yr=1985&lg=nfl",
    'User-Agent'=>'Mozilla/5.0');
my $tree = HTML::TreeBuilder->new;

$tree->parse_content($page->decoded_content);
#$tree->dump;

foreach my $table ($tree->look_down('_tag', 'table')) {
    print "###Table###\n";
    foreach my $row ($table->look_down('_tag', 'tr', sub { $_[0]->look
+_up('_tag', 'table') == $table; })) {
        if ($row->as_text =~ / at /) {
            my $c = 0;
            foreach my $col ($row->look_down('_tag', qr/^t[dh]$/, sub 
+{ $_[0]->look_up('_tag', 'tr') == $row; })) {
                if ($c++) { print " "; }
                printf "%s", $col->as_text;
                if ($col->look_down('href', qr/./)) {
                    printf " [%s]", $col->look_down('href', qr/./)->at
+tr('href');
                }
            }
            print "\n";
        }
        else {
            printf "%s\n", $row->as_text;
        }
    }
}
    
exit;
[download]

When looking for rows and columns, I perform a look_up nexted inside my look_down. This may not be an issue for this webpage, but I deal with a lot of nested tables on my websites, and this eliminates processing a row within a nested table.