According to the PHP Developer's Cookbook there are a variety of new ways you can do various inter-process communication with PHP 4.0, including socket programming, Unix Domain Sockets, UDP/TCP calls, etc. I'm not sure how you'd work that with mod_perl exactly, but you could certainly look into setting up your PHP script to listen for instructions and/or communications whenever the mod_perl is executed.

With PHP 4 the Zend engine is supposed to be much faster than the older PHP engine, although I haven't tried any of the more sophisticated new elements of PHP, so take all this with a grain of salt. =P