then later tried the JRE just in case the JDK did not come with a virtual machine..

hehe

Make sure you are putting the java command, not the path to the JDK, into your $PATH,

eg:
export JAVA_HOME=/opt/IBMJava2-SR10
export PATH=$PATH:/opt/IBMJava2-SR10/bin/java

Yeah i couldn't find much documentation for JEmplode either, but the JDK should have pleanty of docs.