A few small things

It looks you are testing for comments twice.

for (my $nr = 0; $nr < $filearrnr; $nr++) {
    splice (@filearr, $nr, 1) if ($filearr[$nr] =~ /^#/)
}
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and

next if ($filearr[$nr] =~ /^#/);
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You might consider the more perlish, more compact construction

    
foreach my $nrl (@hostarr){}
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instead of:

 
for (my $nr1 = 0; $nr1 < $hostarrnr; $nr1++)
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If you wanted to be moderately fancy you could  fork() each server's FTP session. That way your script wouldn't hang waiting for an unreachable host to time out

email: mandog