That's not a mess... THIS is a mess:

open$x,pop;@x=map{chomp;$_}<$x>;pop@x;map{chomp;$x{$_}++}<>;print map{
+$_,$",$x{$_}||0,$/x2}@x
[download]

when run with your test files yields:

>perl mess.pl testfile1 testfile2
5 3

2 2

3 2

1 0

SCNR