HI,
in my opinion, hibernate that is shiped with jBPM 4.3 should be good enough and you should not mix libs from jBPM 3 with 4.3.
If it comes to j2ee library, could you provide some more information about how you are going to execute your process?
By console, do you mean that you are executing from command line or BPM console?
If you will execute your process from a container (JBoss AS) j2ee lib will be available on runtime.
Cheers,
Maciej