Feature #2710 - clean up use cases

[georgemccabe]

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[j-opatz]

All of the warnings/errors that were occurring within the use cases have been corrected. The only "error" now appearing in the differences of truth to feature branch is due to the change in the configuration file to read in the correct level (since the Python code was also changed to assign the correct level). I have confirmed all of the changes present are necessary and updated the use cases correctly.