Thank you poj for helping me again, now it works like a charm. I have tried to solve the remaining problem by myself like this:

#!/usr/bin/perl 
# Remove extra text from a PGN or Text-file.
use strict;
use warnings;
my $regex = '{\[%tqu[^\]]*]}';
my $line = do { local $/;  <>; }; 
$line =~ s/\n/ /g;            
$line =~ s/$regex//gi;
# these statements I have inserted
$line =~ s/\]/\]\n/g; 
$line =~ s/\[E/\n\[E/g; 
#  end
$line =~ s/ (\d+\. )/\n$1/g;
print $line;
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and it "nearly" worked, but I got an empty first line in the outputfile.