I am not seeing MIDI ports for Pure Data in qjackctl, neither in "Graph" nor "Connections." PD settings has input/output options for qjackctl, MIDI Through-Port 0, and whatever hardware I have plugged in. This works - MIDI Through-Port 0 has my MIDI - but previously, PD had its own ports in qjackctl and Carla. And I liked it!
My qjackctl "Execute after startup" is
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pacmd set-default-sink jack_out && a2jmidid -e &
Also, while we're on the subject, I still don't really understand the MIDI driver options (raw, seq, none). I've tried 'em all.