Regarding the files, I don't know what the files will be named ahead of time so how do I test if the module is loading the correct ones? If I create dummy files to run tests on, it will interfere with the proper operation of the actual module.

Then your module lacks a parameter telling it WHERE to look for the files. During the tests, you want to look for test input files usually below the "t" directory, not where the production files are.

Alexander