That depends... the link can be broken as it should be in your case. You only need to create a link to /usr/bin/java with .java_wrapper ONLY if it is a jvm from www.blackdown.org.
Your version seems to be a different sort. under your java bin directory should be a java, javac, etc that you can link to the /usr/bin directory :

ln -s /usr/lib/j2re1.4.0/bin/java /usr/bin/java

and

ln -s /usr/lib/j2re1.4.0/bin/javac /usr/bin/javac


I have edited my .bash_profile to read:
export Java_HOME=/usr/java/j2re1.4.0._01
export PATH=$JAVA_HOME/bin:$PATH
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
All wrong above. Close but not for *nix useage. It should read:

export JAVA_HOME=/usr/lib/j2re1.4.0
export PATH=$JAVA_HOME/bin:$PATH

or

export JAVA_HOME=/usr/lib/j2re1.4.0_01
export PATH=$JAVA_HOME/bin:$PATH

depending on the actual path to your jvm directory. You have it listed as /usr/lib/j2re1.4.0 in one instance and then have the path listed as j2re1.4.0_01 in another. Everything is predominately case sensitive in *nix (linux, unix, freebsd, etc).
This should fix your problem and I will update/upload the Installation Instructions on how to install using any environment and any jvm from virtually any source. My apologies for not doing this sooner but I was away for a few weeks. Deep in rebuilding my own projects from the ground up.

altoine