One big problem you seem to have is that you have a server with some older versions of perl-modules. Is that a server under your control, i.e. can you update the machine or at least install new versions of the modules?
If yes, then that is the first thing you should do. If no, then there is no real advantage in installing CGI 3.38 on your local machine.
If you want to get rid of modules you installed into /usr/local/share/perl/, you might just delete them and adjust perllocal.pod (see http://www.cpan.org/misc/cpan-faq.html#How_installed_modules).
But I haven't tested this method and can't guarantee its correctness. The absence of the question 'How can I delete a perl module installed by cpan' in the CPAN FAQ might be a warning sign ;-).
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