Try cleaning up perl directories in /usr/local: ubuntu-packaged Perl is installed with /usr prefix, and CPAN is installing everything with /usr/local prefix by default, so you should get your system Perl back if you delete the modules installed in /usr/local/ (Perl searches for its data in /usr/local before /usr).
By the way, if you want to install a newer Perl version, it might be better to use perlbrew or perlall.
Edit: minor spelling corrections
Sorry if my advice was wrong.
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