I'm actually having to edit the code quite badly to allow me to use InputStreamReader to read from the jar. I am actually having difficulty doing this as I am now unsure how to create the JarEntry since it was previously a File for the constructor. However since I'm going to be attempting to read from the Jar, it needs to be some sort of InputStream, which means I cannot get the path of it to create the JarEntry (or at least i can't figure out how).
Also, when I ran my jar the first time, it had the IO Error when trying to find the files before terminating. Unforuntately, it doesn't appear to have released rights over the Jar that was executed AND the Jar it attempted to create, which means I cannot delete them or replace them. I would think I just need to terminate the process, but I am unsure what process that is.