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At the moment if you want to create a new Java project wizard, it's an exercise in reverse engineering and using internal APIs. The wizards and underlying infrastructure should be rewritten so it's easy to reuse pages, add more pages, and add behavior before, during, and after the project creation process.
Moving to JDT/UI
There's 'org.eclipse.jdt.ui.wizards.NewJavaProjectWizardPageOne' and 'org.eclipse.jdt.ui.wizards.NewJavaProjectWizardPageTwo'. Please provide more details, if those don't work for you.
Okay, here's some specific things that should be done: Move the logic of the wizard out of being executed by page two and into the wizard itself. Make the logic understandable, with clear places to insert new behavior. At the very least document the current mess, since it is unreadable. Better would be to create a set of methods on the Java wizard that new wizards can override to insert behavior before or after particular points. Document the whole process of building such a wizard. Expose the necessary pieces as public in bundles so developers don't have to add annotations to ignore access warnings to their plug-ins. That would constitute a good start.
