I second the advice not to mess with the system Perl. But it's your system not mine. I believe you can get the older copies of modules at least somewhat cleaned out by configuring the install arguments. Something like

cpan> o conf make_install_arg UNINST=1
cpan> o conf mbuild_install_arg uninst=1
cpan> o conf commit

may do what you want. I am unsure what will happen if the new kit does not contain all the modules that the old kit contains.