I would need to see your code to guess why data is getting lost, but in general here is how you would split these records as you require(untested):

while (my $line = <DATA>) {
   my @columns = split /\|/, $line;
   push @array1, $columns[1]; # Note the first element [0] is empty
   push @array2, $columns[2];
   push @array3, $columns[3];
}

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|0|PA|1|||BELL|FRANCIS|D|||1||ANGORA||FLEET|HAMPSHIRE|GU51 2UA|
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