For your perl modules installed from ports, you can do something along the lines of portupgrade -f p5-*.

For your bsdpan-* packages, if you'd like to recompile them and switch them to their respective ports distributions to make it a bit easier to maintain, you can do: portupgrade -f -o portdir/p5-Foo-Bar bsdpan-Foo-Bar

So, using a specific example: portupgrade -f -o www/p5-WWW-Mechanize bsdpan-WWW-Mechanize