If you really want to customize your game, you will need to learn how to program in the Java programming language. You can learn more about programming in Java on the internet. A good place to start is this Java tutorial. If that link doesn't work, you might just go to google.com and search for something like "Java Tutorial".
Programming is really hard when you first start learning how to do it, so don't get discouraged. It takes a lot of time (I've been programming for at least 15 years - that's a long time), and a lot of practice.
All of the source code (everything used to program this game, and the editor) is in the learn3D folder. Good programmers usually put comments in their code that helps you figure out what they have done - I was kind of rushed when I wrote this code so I didn't put in many comments... sory :( . The source code is provided under the GPL (GNU public license) which means your allowed to use it and change it however you like.
The other thing to do, if you really really want to customize your game, is study lots of math in school. 3D graphics use a lot of math - especially something called Vector Calculus (oooh scary!)