Also, /usr/bin/perl (which takes precedence over /usr/local/bin/perl) is suspiciously small at 47KB compared to 1203KB for /usr/local/bin/perl.

That's not a problem if it dynamically links to libperl.so. It's 6.8k on my system and works fine.

What would you do to fix this?

Remove all parts of the perl in /usr/local/, and reinstall the one in /usr/bin.

Update: I don't know the package management system that comes with MacOS, but I guess it'll replace /usr/bin/perl. And a small advice for the future: /usr/ is reserved for things come are installed via the package manager; for things compiled from source there's /usr/local/ or /opt/.