First off, Gentoo's system is largely written in Python, not Perl. :-P There are aspects of it in shell, as well, but the base is Python. You may have a few odd tools written in Perl, or C/C++ (like eix), but it's still basically Python/shell.

Second, since the system is written in python, shell, and C (awk, sed, grep, unzip, gcc, etc.), you probably could have just re-emerged perl and any other modules that you needed. Probably easier than what you did :-) If you're maintaining your own parallel setup, it might be worth it to simply copy the existing perl ebuilds to new groups (e.g., dev-perl/myperl and dev-myperl/ and myperl-core), copy over the ebuilds with some minor, automatable difference, and then let portage handle the rest.

Finally, a couple Gentoo/perl must-haves: if you haven't found it yet (it took me years of using Gentoo before someone mentioned this to me), check app-portage/g-cpan. It's entirely worth the effort to set up. Really. It bridges the gap between cpan and portage, making perl module management generally trivial, including uninstall. So when you upgrade from perl 5.8.8 to 5.8.9 or 5.10.0, when they hit the portage tree (5.10.0 is in perl-experimental, though I've not tried it yet), a rebuild of the modules will remove them from /usr/lib/perl5/5.8.8, too.

If you're using KDE (and this can apply to any Linux, not just Gentoo, though it's more important on Gentoo), check out kio_perldoc. If you're on KDE 3.5, you'll have to install it from the source on the webpage, but if you're on KDE 4.1, you can emerge kde-misc/kio_perldoc. If you're on the alpha of KDE 4.2 (aka 4.1.80), it's been integrated, on all distros, into the core KDE (in the split-build of Gentoo, it's in kde-base/kdesdk-kioslaves). It allows you to read the perldoc from konqueror using "perldoc:/File::Spec", for example. Important on Gentoo where "man File::Spec" doesn't work (but perldoc File::Spec does). (I got the gentoo devs to put it in for KDE 4.0 and 4.1, and reminded the original author to check it in for 4.2.)

Just my thoughts from running Gentoo for about 3.5 years, on what's now four machines...