The solution I came up with was to not use the header input for HTML::TableExtract then in the foreach loop call out the column number I wanted. This also required me to skip the first line (as that is the header information) so I added that counter. It's a simple solution, but I'd still be interested in knowing if there is a way to do this through the module:

 my $i=0;
 foreach my $ts ($te->table_states) {
   $i++; next if $i==1;
   print "Table (", join(',', $ts->coords), "):\n";
   foreach my $row ($ts->rows) {
   foreach (@$row) {
       tr{\t\r\n\xAO}{ }s;
       s{^\s+}{};
       s{\s+$}{};
   }
   print "@$row[2] @$row[4]";
   }
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