This is not true for the 2nd generation LS, right?Yup, same. If you get arms from a dealer they'll have Jag cast on them.
Generally the 98-02 S-Type suspension swaps with the LS and Thunderbird suspension, except:
front springs are different, so front shock spring pockets are different
front lower arms are sometimes different
shock rates are different, but mounting is the same
It's unclear to me if the S-type had a ""sport"", so I would be extra careful on stuff like sway bar sizes.