で、今回一番めんどいのは上の方でもちょっと出たけど、これかなぁ。
5.4Rになったこととは直接には関係しないけど、影響でかいし。

20050201:
AFFECTS: users of lang/perl5 and lang/perl5.8
AUTHOR: tobez@FreeBSD.org

lang/perl5 has been updated to 5.6.2, and lang/perl5.8 has been
updated to 5.8.6. you should update everything depending on perl, that
is:

* first, upgrade your perl installation (use either lang/perl5 or
lang/perl5.8, the latter being recommended);
* for FreeBSD 4.X, run "use.perl port", so that the system knows you
have 5.8.6 or 5.6.2; this step is not needed on FreeBSD 5.X and
FreeBSD -CURRENT;
* run some magic incantations to upgrade all ports depending on perl,
that is run something like :
portupgrade -f `(pkg_info -R perl-5\* |tail +4; \
find /usr/local/lib/perl5/site_perl/5.[68].[1245] -type f -print0 \
| xargs -0 pkg_which -fv | sed -e '/: ?/d' -e 's/.*: //')|sort -u`
This is likely to fail for a few ports, you'll have to upgrade them
afterwards by hand.