• Scripts reside in server A (Has Perl modules installed)
• Webserver is B (no Perl and policy said we can't install)

What sort of environment are you running in that won't allow Perl to be installed (or doesn't already have Perl installed?)

Once solution to this would be to convert your scripts on Server A into a web service and communicate back to the PHP scripts running on Server B via JSON encoded messages or some such.

Take a look at the path_info() method of the module CGI for some ideas on how to implement this. It is a quick and dirty way of implementing something that sorta looks like a RESTFull service.