Because I could not find it I created it... and now to share it!
I have attached the JMX config files for monitoring Boomi Atoms and Molecules via the Splunkbase App - Monitoring of Java Virtual Machines with JMX.
The config files are set up as clusters. At the bottom of the file, define the connection information and all defined metrics will be queried for each server defined in the cluster. I have included most if not all of the recommended metrics discussed in the Boomi article "System Monitoring with JMX" plus additional metrics I found interesting. Due to the differences in an Atom vs Molecule, the metrics vary slightly between the two.