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