Thank you for your response.
I should add that I can see the script continuing to processes in the background on the server, just the web page seems to timeout. If I limit the script so it has a smaller set of items to complete it completes just fine and displays the response.
If I monitor script progress for completion, and then check for my finished files it all works fine, I just don't get the feedback from the script because the page times out.
I'm thinking apache/PHP is timing out the response somehow. Like I said in the original post, this worked prior to my EC2 instance change.
P.S to your point, I've put logging in and the script executes fine, I just don't get the output on screen if the page times out.