Perl.com has an excellent article on speeding up Perl programs: what we can and can't help with:
A well-written Perl program should, in theory, beat a shell script, right? In theory. In practice, sometimes the details of your Perl installation have more to do with why your program is slow than you might believe. Jean-Louis Leroy recently tracked down a bottleneck and wrote up his experiences with making Perl programs start faster.