Okay, I have solved the frequency sorting by changing the prints to push. Then getting an array and joining the headers and allsentences. Then sorting by length.:

    #5# ....
                        push (@allsents, "MATCH #$count $sentmatches[$
+m]") unless $seens{ $sentmatches[$m] }++;
                        $count++;
                        
                    }
                }
                push (@sepmatches, @allsents);
                
                ##$allmatches[0] is header, [1] is all sentences etc. 
+EVEN - header, ODD - sent
                ## Now join headers and sentences (0 and 1 etc.)
                foreach (@sepmatches) { ##Try Use natatime where n=2
                    $joinmatches = join ('', @sepmatches);
                }
                push (@allmatches, $joinmatches);
                @sortedallmatches = sort {length $b cmp length $a} @al
+lmatches;
                
            }
        }
    }
     print @sortedallmatches;
}
[download]

The messy part (though it's all pretty messy) is that I had to call the @allmatches after the first for loop so it would not print every result every time. Then call @sepmatches after the second for loop

Thanks for the help PM, I hope to join the ranks when I know a little more Perl!