My recommendation would be to leave the system
perl alone, since, as you found out, it is often important to the running of the system. Then you can compile and install from the latest source (pretty easy!), available at http://www.perl.org/, just being sure to set it to install to a different directory from the system's
perl. The help files that come with the download are pretty good at explaining everything that needs to be done.
Alternatively, if you just need Perl installed for a single user, you can use Perlbrew which will automatically download and install a variety of Perl versions in a user's home directory, though this is configurable:
The default perlbrew root directory is ~/perl5/perlbrew, which can be changed by setting PERLBREW_ROOT
You can use the system's
cpan to install Perlbrew itself, or use the commands given on the Perlbrew website.
ActiveState also offers binary downloads for Linux at this site, if you don't want to build from source.