Not naive.  Most temporary cements contain eugenol (equivalent to oil
of cloves).  I can't say I've seen a lot of sensitivity to it, but
certainly anything's possible.  Furthermore, most temporary crowns are
fabricated from some form of acrylic plastic.  Certainly any free
monomer may be irritating to some people.
    The temporary cement and/ or any free monomer can cause the taste.  If
the temporary isn't smooth it may promote food implaction which also has
potential to cause bad tastes.
    It is not unusual to irritate the gumline in the course of preparing
and impressioning the tooth itself, so soreness here may be due to
mechanical as well as chemical trauma.  It should heal in a few days if
this is the case.  If this is a lower molar this can sometimes be
confused with a sore throat.
    There is obviously no way for me to know if I would make the same
decisions with regard to replacing the crowns.  But you deserve to know
WHY they are being replaced, in language you can understand.

Steve