Hi. I've updated my ("amd64") patchset against ninjam-with-jack 0.0.2, use at own risk, etc. It's for use with an amd64 debian host and the GNU GCC 4.x compiler series.
On the matter of JACK input/output ports, I might see the usefulness of bypassing the ninjam mixer, or providing ninjam mixer inserts using JACK ports. It's kind of overkill if you ask me though. That is, unless you are supporting 5.1 sound channels and then it becomes more immersive
-Eric