One other thing, if you're going to go that route, would be to consider consolidating all the exclude strings into one pattern. Something like this.

if (@strings){
  $re = join "|", map {quotemeta} @strings;
} else {
  $re = undef;
}

foreach my $line (@file1only) {
    print unless defined($re) && /$re/;
}
[download]