Hello Paul!
 No my sequencer's ports don'te really appear. they appear, when they are connected to somthing.
 I now did it like this:
 I saw that jack_midi_clock was automatically connected to
j2a_bridge:playback
 In ALSA I have port 129 listed with "aconnect -li".
 So I asked my sequencer to connect to 129 and get its clock source there. The rest of the sequencer connections were pure ALSa for the test.
 Then I started jack_transport and told it to "play".
 Nothing happened, yet that might be due to the clock. But would you say, that this setup looks sane?