Hmm, just something that might help simplify quite a bit your program.

     if ($line =~ m/^A.TL5E00/)    
     {
     $line =~ s/A.TL5E00/+TL\E5C/g;      
     push @NewSym,$line;
     }
[download]

might probably be rewritten in a simpler fashion:

     push @NewSym, $line if $line =~ s/^A.TL5E00/+TL\E5C/g;
[download]

I haven't tested it on real data (you did not supply any), but it seems to work properly, as shown in this session under the Perl debugger:

$ perl -de 42

Loading DB routines from perl5db.pl version 1.33
Editor support available.

Enter h or `h h' for help, or `man perldebug' for more help.

main::(-e:1):   42
  DB<1> $line = "A.TL5E00xxxx";

  DB<2> push @NewSym, $line if $line =~ s/^A.TL5E00/+TL\E5C/g;

  DB<3> x @NewSym
0  '+TL5Cxxxx'
[download]

If the substitution does not find a match, it will report a false value and the push will not be executed.