Untested: 
%data;
$data{$_[0]}{$_[1]} = [@{$_}[2,3]] for @$query2;
foreach my $row (@$query) {
    no warnings 'uninitialized';
    $$row[2] -= $data{$$row[0]}{$$row[1]}[0];
    $$row[3] -= $data{$$row[0]}{$$row[1]}[1];
    local $" = ",";
    print "@$row\n";
}

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In reply to Re: array of arrays calculations by JavaFan
in thread array of arrays calculations by rocky13

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