We're getting ready to go from 5.6.1 to 5.8.6, so I'm dealing with some of the same issues. I posted a while back for some initial guidance in the node: Maintaining an Enterprise Perl Distribution. I plan to post more detail on what we did and how it went after we convert. We're probably going to start the actual work in June.

We're also looking at Apache 2 and mod_perl 2, but I agree with the suggestions to limit how much you change at once. On that note, you may want to consider re-installing only the modules you really use. Monks provided some guidance on that in this node: What modules are we actually using?.

Good luck!