Private Client File System Upload Area & Admin Script Execution

Hey All - love the themes and plugins. I have been trying to find a solution to my client's project. I installed WP-Client which offers most of the features I need. (private client file system and client upload center) My issue is that I have written a script that acts on the files in the private file system (that the client has uploaded) - parses and compares all the data - and returns reports. Any ideas how to integrate these features? I'm at a loss and their support is less than helpful. Thank you in advance!