This section is a boiled down version of everything above. It should serve as an easy reference. These steps assume you've identified and installed the correct JDK.

1. Locate the jar file: Extender > Extensions > Select extension > Details. bapps\ directory is located at C:\Users\yourusername\AppData\Roaming\BurpSuite\bapps
2. Backup the original jar file to a different folder, outside of bapps.
3. Change extension from .jar to .zip, extract contents, delete .zip file
4. Make your modifications
5. Re-jar: jar cvf yourJarName.jar -C extractedContentsDirectory/ .