This project is to build a real-time list of differences in the server environments (file system, PHP, Apache, Mysqld) between [SERVER A], the desired environment and [SERVER B], the environment that will become like [SERVER A]. Thoroughness and attention to detail are important when notating the differences.
You should prepare a mechanism to create a report listing these web app environment differences, so that our system administrator can bring [SERVER B] up to the same configuration as [SERVER A]. In all cases, [SERVER A] will have the "master" configuration, with [SERVER B] conforming to it, not vice-versa.
There may be other approaches to this problem but I would expect the easiest way to tackle this objective would be to create a PHP script to expose the environmental configuration and variables for PHP, apache, Mysql, as well as the filesystem files, and then use this to compare against another server's result.