I think you need to back up here just a little bit and ask what about this project requires you to use Perl or is more easily done with Perl? If your answer is I don't know, I just want to use Perl, then I think you should stick with PHP. Perl is extremely useful, but I have yet to see a web project where Perl was a better option than PHP.
As for including files, I alwasy found that using mod_perl and ePerl (more info) worked better than just using perl from cgi-bin. You can simply include a file with Apache's SSI with this method. You of course can do it the way others have mentioned above.