I created a custom Linux AMI with all I need to run my PHP app (basically a node that does batch processing of images/video/audio). There can be n amount of instances running at the same time. So far it deploys and works fine.
My only concern is that I had to hardcode a few MySQL DB credentials, FTP passwords, and other things that might change in the future. I have other servers where these credentials could be made available (outside Amazon's network) but I'm not sure hot to get these credentials into the EC2 instance after I start it up. These should be easy and secure for a new EC2 instance to get but not for anybody else.