If you've installed into /usr/local, it's unlikely that you've overwritten any "system files", as Ubuntu system files aren't installed into /usr/local.

So, just rename /usr/local/bin/perl to somethink else like /usr/local/bin/perl5.12.3 and be done.  As saying "perl" will now no longer find the new perl along the PATH, there's no need to remove it. And you could even call /usr/local/bin/perl5.12.3 in case you should want to test something with the newer version.