It sounds like you'll be learning with either language, so you really are in the advantageous position of deciding where your career might go. If you want to become proficient with PHP, do you web site with PHP. If you want to become proficient with perl, CGI, and mod_perl, do your project in Perl. The Monks are always here for you.

Neither will become obsolete and either one can get the job done. If something tips it one way for me, it's that you already have some Perl experience. If you're new to the web side of things, you'll be exposed to so many new things to learn, you may find comfort in what you already know. You'll likely spend less time with trivial issues if you stick with Perl.