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;
and it "nearly" worked, but I got an empty first line in the outputfile.