Since you give no usage what so ever, i can only speculate just exactly what you want to output to look like. And more importantly, what the "rules" are. But i can say that you have a lot of needless code there. Try this instead:

use Data::Dumper;

my (%symbol,@old,@new);
my $max          = 10;
my $ws_replace   = '_';
my $letters_only = 1;

while (<DATA>) {
   chomp;
   push @old, $_;
   $_ = substr $_,0,10 if $max;
   s/\s+/$ws_replace/g if $ws_replace;
   s/\W+//g            if $letters_only;
   $_ .= $.            if $symbol{$_}++;
   push @new, $_;
}

print Dumper \@old, \@new;

my %compare;
@compare{@old} = @new;

print Dumper \@compare;

__DATA__
Line one
Line two
xxxxxxxxxxx
Another line
xxxxxxxxxxx
Lines end here not
xxxxxxxxxxx
Fourth line (used to be)
Line five
Lines end here
Lines end here too
[download]

L-LL-L--L-LL-L--L-LL-L--
-R--R-RR-R--R-RR-R--R-RR
B--B--B--B--B--B--B--B--
H---H---H---H---H---H---
(the triplet paradiddle with high-hat)

I'm puzzled.

Why would I want to do this? I've looked at this several times over the past couple days trying to figure out the point. Can you explain what you mean to actually use this for? My "code smell" sniffer keeps wanting to tell me you are working up to symbolic references and the like.