I've been searching around, and my original questions on the ubuntuforums are long gone (I think they had a security issue and the old forum was scrapped a number of years ago. But I did find an old post related to qjackctl.
http://www.rncbc.org/drupal/node/180
But you are starting jack from Reaper directly - so you would need to just open a terminal and run alsa_in from there (after Reaper starts jack). Also, in that post I mention alsa_in was only included in Jack1 - that's definitely not the case, as it is installed with Jack2 in ubuntu these days.
At any rate, alsa_in adds channels from another alsa card to the card that jack is using. In the qjackctl post from 2010, I mention my command was "alsa_in -d hw:1". In that case I was trying to add my Alsesis Multimix to the onboard sound of the laptop. hw:0 was the first card started in jack. Alsa_in added hw:1, the second card to that. There's other modifiers that can be added, but keeping it simple like that worked well enough for recording 3 minute power pop songs, even with 2 unlinked usb interfaces. From your alsa info above, it looks like you would need "alsa_in -d hw:3"if jack is using your other Audiophile hw:1.
A useful link about alsa_in and Alsa_out:
http://www.penguinproducer.com/Blog/...ces-with-jack/
But reading about zita_ajbridge, it may be able to do the same, but better. Never used that, though.
https://kokkinizita.linuxaudio.org/l...uickguide.html