This is as much a perl question as it is a linux question. The most annoying part of upgrading perl is making sure all your installed packages will still work with the new one, especially given the binary compatibility shenanigans that have been going on with the low 5.8.x's

For instance, had I known about perl -MCPAN -e autobundle earlier, I could've saved myself a lot of headaches involved in these upgrades.

Your second example assumes that the Linux distribution in question is rpm based, which is not necessarily the case (would've helped if the OP mentioned the specific flavour); even if it is, perl itself could've been installed from source, for a variety of reasons (for example, RedHat has been shipping with an oddly compiled perl for a long time, one of the biggest problems being that large file support was turned off for whatever reason).

If the installed (and the new) perl wasn't prepackaged by the system vendor, it would help to examine the output of perl -V to match the new environment to the old one.