I always side with a clean build if possible....that way Tomcat, Java, etc get put on the way they were meant to with the installers.
That way it also forces thought about antivirus, backups, vm guest tools, system resources, clustering, etc.
I would make sure to follow the article above and keep a full, accessible backup (in addition to the database dump) of the old box/VM for the easily forgotten stuff such as Keystores, Tomcat customizations, etc.
As devils advocate, I would double check that Jamf, Tomcat, java and MySQL are supported on Win2k16. Likely are but I would be pedantic and check all of that on an important server such as this.
