Hello Tim.
First of all, congratulation with your game. It looks really attractive.
Related to your Java 3D question. You should be aware of some facts related to Java3D. It is an old API which is not open source previously. I think it is a great API and valuable for Java but it does not have any active community and it is not improved as far as i know. Only some bugfixes performed rarely by one person as far as i know. So, you might consider learning better 3D APIs for Java. I am not an expert on graphics but community is very important for open source projects. And as far as i know,
jME has a better community and much more actively developed. You can search for other ones too.
Regarding Java3D javadoc, yes it had one and it should be on java.net. Please check java.net project page again and PM me if you still can not find it.
For further Java3D documentation, please check following urls:
Java 3D API Tutorial
http://www.freebooksource.com/JAVA/O...rogramming.htm (You can download this book from rapidshare link there.)
Pro Java 6 3D Game Development: Java 3D, JOGL, JInput and JOAL APIs - IT-Guru (Another rapidshare link for a book)
You can try searching amazon. There should be a few more related books.