Jill,
It's probably best to recreate the perl functionality with PHP.
cUrl is a nifty utility for remote URL connections and allows you to GET/POST data as well as send/recieve cookies. I use this all the time to connect to remote site and parse them, plus it gives nice responses and allows you to read the server response headers.
If you must use the perl script, it's possible that by doing some tweaking, you could get the script to work better with your PHP script.
One thing you can do is have PHP call the perl script multiple times, one for each page request, it can then take each request result and parse it before handing it to the user.
But regardless of what direction is taken, the end result needs to be one where PHP can grab each result, parse and output before starting the process over again.
This thread has already fallen off the page,
so feel free to email me and we can go over it via chat or something.