importing and running it. Py2exe automatically sees this and bundles all of the .py files for the application. I'm assuming this means I would need to use a separate importer in the same manner as with the module files to import and run the application when it is updated.

yes. That may even save you the preloader.
Look at the exclude - parameters, often it is possible to stop py2exe from including stuff.

I recommend to read the py2exe source, especially the part of the components py2exe puts into the startup of the resulting .exe. Reading those few pages of code will make your problem solving much faster.

Harald Armin Massa
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Amtsgericht Stuttgart, HRB 734971
et programmare