Ok, given your situation and your claim that shared memory is faster, the proxy model might makes sense.

Machine A

PHP ⇐|
PHP ⇐|  
PHP ⇐|⇒ Perl Proxy ⇐|
PHP ⇐|              |
PHP ⇐|              |
                    |
Machine B           |⇒ Perl Processor
                    |
PHP ⇐|              |
PHP ⇐|              |
PHP ⇐|⇒ Perl Proxy ⇐|
PHP ⇐|
PHP ⇐|

When I say "your claim that shared memory is faster", I don't mean to imply that it's false, just that I don't know it to be true or false. And it seems that you haven't included the time required to synchronise the local threads/processes and the time required to signal/detect a change in the shared memory.

Can they facilitate a request/return type system to an already running script?

A named pipe could, kinda, but a unix socket would be better.