Instead of trying to do everything with a single regular expression, consider breaking it up into two.

$str =~ s/\[id=(\d+)\]/<a href='...$1'>/g;
$str =~ s/\[\/id\]/<\/a>/g;
print $str;
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This will deal more gracefully with links that span multiple lines (which often happens when people write in a auto-wrapping editor.)