1. Almost all the simulation were integrated with RK4.
2. Most of the second order ODE should be able to break into two first order equation.
3. I would suggest you try [url=http://www.phy.ntnu.edu.tw/ntnujava/index.php?board=11.0]Easy Java Simulations (EJS)[/url].
The code you got was created almost 10 years ago with JDK1.0.2. I switch to EJS since 2001 and it will be much easier for non-programmer to create simulation.