As far as I know hibernate included in jbpm 4.3 is 3.x.x so it should be quite ok to use it instead of the one bundled in jBpm 3.x but the easiest would be to check hibernate docs about these two versions.
About j2ee.jar perhaps you don't need to include complete package of j2ee but only required parts of it (jta, ejb, etc) that can be found as separate jars as well.