The only error a missing tools.jar will cause is failure to compile jsp pages. I would assume the /usr/java/j2sdk1.4.2_02 installation is corrupt. List the contents of the /usr/java/j2sdk1.4.2_02/lib directory.
My mistake. It's a case of just setting the JAVA_HOME variable correctly for the user that's running the application. Because run.sh is being called to run as a different user, the JAVA_HOME variable for that user isn't set correctly, even though the user that's calling the script has it set correctly.