Did I just mess up system Perl?
Most probably you did not do anything harmful. It would be easier to tell if you can remember which CPAN commands, you've entered.

It is perfectly normal that the first run of CPAN creates the directories mentioned, downloads various files containing package indexes, etc. It potentially also updates various packages that forms the basis of CPAN itself, as well as packages that are depended on by the Lchown package, you're trying to install.

All in all - you're most probably completely fine.