So how did you make it work in Tomcat? Was it a matter of using xalan 2.7.1 and corresponding serializer.jar?
You need make sure xalan 2.7.1 and corresponding serializer.jar are available to docx4j in JIRA... Which version of JIRA are you using, and which Xalan, if any, does it ship with?
Re 25485, docx4j should be able to use Xalan (as opposed to Saxon) provided it is there.
Please let us know how you resolve this, or feel free to post with further data