Do I need to make deinstall all of these ports and start all over?
I'd appreciate someone correcting me if I'm wrong; I think you should
just be able to upgrade your ports tree (directions in the Handbook) and
then the ports will compile with the latest versions.

That should be the case, yes. I occasionally use portupgrade, and occasionally do upgrading directly from the Ports tree, and haven't had any issues with it yet. pkg_version and friends still work great, and when I want to use portupgrade it still works, even if I previously upgraded straight from the ports tree (a la 'cd /usr/ports/ category/port && make && make install')
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