You can use JBPM for workflow and persistance. Infact JBPM as name suggest is BPM. Drools is tightly integrated with JBPM but it is a seperate proudct with seperate binaries.
JBPM console, Govnor are seperate wars and you dont need to use them. You can simply use JBPM binaries as a embeded BPM engine in your application.
JBPM uses JPA and you can can use Hibernate as JPA provider. I believe you can also use your transaction manager but for JBOSS, its transaction manager is recommended.
As per my understanding modifying JBPM to use somthing else instead of entitymanager will need good amount of effort and will need understanding of the source.