While setting up a Java application to communicate with MongoDB, Kerberos and SSL encryption, several key components must be considered, including the KDC server configuration, MongoDB server setup, and the Java application itself. The process involves creating a certificate store for Java, configuring the Kerberos principal password on the application server, compiling and running the Java program, and troubleshooting potential issues such as authentication exceptions. To simplify this complex setup, it is recommended to read through the MongoDB Security Checklist and 12 tips for going into production, which outline recommended security measures to protect your MongoDB installation. Additionally, the MongoDB team provides further assistance through their Google Groups channel.